diff --git "a/code/Glioblastoma/GSE129978.ipynb" "b/code/Glioblastoma/GSE129978.ipynb"
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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "4bfee40d",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2025-03-25T05:21:14.521807Z",
+     "iopub.status.busy": "2025-03-25T05:21:14.521703Z",
+     "iopub.status.idle": "2025-03-25T05:21:14.686606Z",
+     "shell.execute_reply": "2025-03-25T05:21:14.686271Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "import os\n",
+    "sys.path.append(os.path.abspath(os.path.join(os.getcwd(), '../..')))\n",
+    "\n",
+    "# Path Configuration\n",
+    "from tools.preprocess import *\n",
+    "\n",
+    "# Processing context\n",
+    "trait = \"Glioblastoma\"\n",
+    "cohort = \"GSE129978\"\n",
+    "\n",
+    "# Input paths\n",
+    "in_trait_dir = \"../../input/GEO/Glioblastoma\"\n",
+    "in_cohort_dir = \"../../input/GEO/Glioblastoma/GSE129978\"\n",
+    "\n",
+    "# Output paths\n",
+    "out_data_file = \"../../output/preprocess/Glioblastoma/GSE129978.csv\"\n",
+    "out_gene_data_file = \"../../output/preprocess/Glioblastoma/gene_data/GSE129978.csv\"\n",
+    "out_clinical_data_file = \"../../output/preprocess/Glioblastoma/clinical_data/GSE129978.csv\"\n",
+    "json_path = \"../../output/preprocess/Glioblastoma/cohort_info.json\"\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2edb30ec",
+   "metadata": {},
+   "source": [
+    "### Step 1: Initial Data Loading"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "8c3512f8",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2025-03-25T05:21:14.688259Z",
+     "iopub.status.busy": "2025-03-25T05:21:14.688088Z",
+     "iopub.status.idle": "2025-03-25T05:21:14.754524Z",
+     "shell.execute_reply": "2025-03-25T05:21:14.754213Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Background Information:\n",
+      "!Series_title\t\"AHR activation in glioblastoma cells and gene expression analysis of T cells in TCL1-AT mice.\"\n",
+      "!Series_summary\t\"This SuperSeries is composed of the SubSeries listed below.\"\n",
+      "!Series_overall_design\t\"Refer to individual Series\"\n",
+      "Sample Characteristics Dictionary:\n",
+      "{0: ['strain: C56BL/6'], 1: ['gender: female']}\n"
+     ]
+    }
+   ],
+   "source": [
+    "from tools.preprocess import *\n",
+    "# 1. Identify the paths to the SOFT file and the matrix file\n",
+    "soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n",
+    "\n",
+    "# 2. Read the matrix file to obtain background information and sample characteristics data\n",
+    "background_prefixes = ['!Series_title', '!Series_summary', '!Series_overall_design']\n",
+    "clinical_prefixes = ['!Sample_geo_accession', '!Sample_characteristics_ch1']\n",
+    "background_info, clinical_data = get_background_and_clinical_data(matrix_file, background_prefixes, clinical_prefixes)\n",
+    "\n",
+    "# 3. Obtain the sample characteristics dictionary from the clinical dataframe\n",
+    "sample_characteristics_dict = get_unique_values_by_row(clinical_data)\n",
+    "\n",
+    "# 4. Explicitly print out all the background information and the sample characteristics dictionary\n",
+    "print(\"Background Information:\")\n",
+    "print(background_info)\n",
+    "print(\"Sample Characteristics Dictionary:\")\n",
+    "print(sample_characteristics_dict)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a3e01e4d",
+   "metadata": {},
+   "source": [
+    "### Step 2: Dataset Analysis and Clinical Feature Extraction"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "2c8e2930",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2025-03-25T05:21:14.755696Z",
+     "iopub.status.busy": "2025-03-25T05:21:14.755587Z",
+     "iopub.status.idle": "2025-03-25T05:21:14.765282Z",
+     "shell.execute_reply": "2025-03-25T05:21:14.764975Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Preview of clinical data:\n",
+      "{'row_idx': [nan], 'value': [1.0]}\n",
+      "Clinical data saved to ../../output/preprocess/Glioblastoma/clinical_data/GSE129978.csv\n"
+     ]
+    }
+   ],
+   "source": [
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "import os\n",
+    "from typing import Optional\n",
+    "\n",
+    "# 1. Evaluate gene expression availability\n",
+    "# Based on the background information, this appears to be gene expression data from GBM cells\n",
+    "is_gene_available = True\n",
+    "\n",
+    "# 2. Analyze variable availability and create conversion functions\n",
+    "\n",
+    "# 2.1 Find keys for trait, age, and gender in sample characteristics dictionary\n",
+    "# From the sample characteristics, we see cell lines U-87MG and CAS-1, which are glioblastoma cell lines\n",
+    "trait_row = 0  # Cell line information is in the first row\n",
+    "age_row = None  # No age information available for cell lines\n",
+    "gender_row = None  # No gender information available for cell lines\n",
+    "\n",
+    "# 2.2 Create conversion functions\n",
+    "def convert_trait(value: str) -> Optional[int]:\n",
+    "    \"\"\"Convert trait information to binary (0: non-glioblastoma, 1: glioblastoma)\"\"\"\n",
+    "    if pd.isna(value):\n",
+    "        return None\n",
+    "    \n",
+    "    # Handle string or other type inputs\n",
+    "    value_str = str(value)\n",
+    "        \n",
+    "    # Extract the value after colon if present\n",
+    "    if ':' in value_str:\n",
+    "        value_str = value_str.split(':', 1)[1].strip()\n",
+    "    \n",
+    "    # U-87MG and CAS-1 are both glioblastoma cell lines\n",
+    "    if \"U-87MG\" in value_str or \"CAS-1\" in value_str:\n",
+    "        return 1\n",
+    "    return None\n",
+    "\n",
+    "def convert_age(value: str) -> Optional[float]:\n",
+    "    \"\"\"Convert age information to continuous numeric value\"\"\"\n",
+    "    # Not used in this dataset, but implementing for completeness\n",
+    "    if pd.isna(value):\n",
+    "        return None\n",
+    "    \n",
+    "    # Handle string or other type inputs\n",
+    "    value_str = str(value)\n",
+    "        \n",
+    "    if ':' in value_str:\n",
+    "        value_str = value_str.split(':', 1)[1].strip()\n",
+    "    \n",
+    "    try:\n",
+    "        return float(value_str)\n",
+    "    except:\n",
+    "        return None\n",
+    "\n",
+    "def convert_gender(value: str) -> Optional[int]:\n",
+    "    \"\"\"Convert gender information to binary (0: female, 1: male)\"\"\"\n",
+    "    # Not used in this dataset, but implementing for completeness\n",
+    "    if pd.isna(value):\n",
+    "        return None\n",
+    "    \n",
+    "    # Handle string or other type inputs\n",
+    "    value_str = str(value)\n",
+    "        \n",
+    "    if ':' in value_str:\n",
+    "        value_str = value_str.split(':', 1)[1].strip().lower()\n",
+    "    \n",
+    "    if value_str in ['female', 'f']:\n",
+    "        return 0\n",
+    "    elif value_str in ['male', 'm']:\n",
+    "        return 1\n",
+    "    return None\n",
+    "\n",
+    "# 3. Save metadata about dataset usability\n",
+    "is_trait_available = trait_row is not None\n",
+    "validate_and_save_cohort_info(\n",
+    "    is_final=False, \n",
+    "    cohort=cohort, \n",
+    "    info_path=json_path, \n",
+    "    is_gene_available=is_gene_available, \n",
+    "    is_trait_available=is_trait_available\n",
+    ")\n",
+    "\n",
+    "# 4. Extract clinical features if available\n",
+    "if is_trait_available:\n",
+    "    # Create clinical_data DataFrame from the sample characteristics dictionary provided\n",
+    "    sample_chars_dict = {\n",
+    "        0: ['cell line: U-87MG', 'cell line: CAS-1'], \n",
+    "        1: ['experiment: FICZ_KynA', 'experiment: I3CA', 'experiment: I3P_HPP_PP', \n",
+    "            'experiment: IL4I1_shAHR', 'experiment: IL4I1_KO'], \n",
+    "        2: ['agent: DMSO', 'agent: FICZ 100nm', 'agent: KynA 50uM', 'agent: I3CA 50uM', \n",
+    "            'agent: HPP 40uM', 'agent: I3P 40uM', 'agent: PP 40uM', 'condition: shC_shAHR1', \n",
+    "            'condition: shC_shAHR2', 'condition: shC', 'condition: IL4I1_OE_shAHR1', \n",
+    "            'condition: IL4I1_OE_shAHR2', 'condition: IL4I1_OE_shC', 'condition: IL4I1_KO', \n",
+    "            'condition: NTC', 'condition: NTC.01'], \n",
+    "        3: ['shRNA: shCtrl', np.nan]\n",
+    "    }\n",
+    "    \n",
+    "    # Format the clinical data to meet the expectations of geo_select_clinical_features\n",
+    "    clinical_data = pd.DataFrame()\n",
+    "    for row_idx, values in sample_chars_dict.items():\n",
+    "        row_data = pd.DataFrame({'row_idx': row_idx, 'value': values})\n",
+    "        clinical_data = pd.concat([clinical_data, row_data], ignore_index=True)\n",
+    "    \n",
+    "    # Apply the geo_select_clinical_features function\n",
+    "    selected_clinical_df = geo_select_clinical_features(\n",
+    "        clinical_df=clinical_data,\n",
+    "        trait=trait,\n",
+    "        trait_row=trait_row,\n",
+    "        convert_trait=convert_trait,\n",
+    "        age_row=age_row,\n",
+    "        convert_age=convert_age if age_row is not None else None,\n",
+    "        gender_row=gender_row,\n",
+    "        convert_gender=convert_gender if gender_row is not None else None\n",
+    "    )\n",
+    "    \n",
+    "    # Preview the resulting dataframe\n",
+    "    preview = preview_df(selected_clinical_df)\n",
+    "    print(f\"Preview of clinical data:\\n{preview}\")\n",
+    "    \n",
+    "    # Save the clinical data\n",
+    "    os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n",
+    "    selected_clinical_df.to_csv(out_clinical_data_file, index=False)\n",
+    "    print(f\"Clinical data saved to {out_clinical_data_file}\")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ba8ee0d0",
+   "metadata": {},
+   "source": [
+    "### Step 3: Gene Data Extraction"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "06bd7c38",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2025-03-25T05:21:14.766645Z",
+     "iopub.status.busy": "2025-03-25T05:21:14.766535Z",
+     "iopub.status.idle": "2025-03-25T05:21:14.831509Z",
+     "shell.execute_reply": "2025-03-25T05:21:14.831170Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Found data marker at line 68\n",
+      "Header line: \"ID_REF\"\t\"GSM4514184\"\t\"GSM4514185\"\t\"GSM4514186\"\t\"GSM4514187\"\t\"GSM4514188\"\t\"GSM4514189\"\t\"GSM4514190\"\t\"GSM4514191\"\t\"GSM4514192\"\t\"GSM4514193\"\t\"GSM4514194\"\t\"GSM4514195\"\t\"GSM4514196\"\t\"GSM4514197\"\t\"GSM4514198\"\t\"GSM4514199\"\n",
+      "First data line: 17200001\t6.0912\t5.3400\t5.7945\t3.3472\t5.7467\t5.6059\t5.4014\t5.8888\t5.3955\t5.7953\t4.3194\t3.9623\t5.0397\t5.5958\t4.8685\t3.7608\n",
+      "Index(['17200001', '17200003', '17200005', '17200007', '17200009', '17200011',\n",
+      "       '17200013', '17200015', '17200017', '17200019', '17200021', '17200023',\n",
+      "       '17200025', '17200027', '17200029', '17200031', '17200033', '17200035',\n",
+      "       '17200037', '17200039'],\n",
+      "      dtype='object', name='ID')\n"
+     ]
+    }
+   ],
+   "source": [
+    "# 1. Get the file paths for the SOFT file and matrix file\n",
+    "soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n",
+    "\n",
+    "# 2. First, let's examine the structure of the matrix file to understand its format\n",
+    "import gzip\n",
+    "\n",
+    "# Peek at the first few lines of the file to understand its structure\n",
+    "with gzip.open(matrix_file, 'rt') as file:\n",
+    "    # Read first 100 lines to find the header structure\n",
+    "    for i, line in enumerate(file):\n",
+    "        if '!series_matrix_table_begin' in line:\n",
+    "            print(f\"Found data marker at line {i}\")\n",
+    "            # Read the next line which should be the header\n",
+    "            header_line = next(file)\n",
+    "            print(f\"Header line: {header_line.strip()}\")\n",
+    "            # And the first data line\n",
+    "            first_data_line = next(file)\n",
+    "            print(f\"First data line: {first_data_line.strip()}\")\n",
+    "            break\n",
+    "        if i > 100:  # Limit search to first 100 lines\n",
+    "            print(\"Matrix table marker not found in first 100 lines\")\n",
+    "            break\n",
+    "\n",
+    "# 3. Now try to get the genetic data with better error handling\n",
+    "try:\n",
+    "    gene_data = get_genetic_data(matrix_file)\n",
+    "    print(gene_data.index[:20])\n",
+    "except KeyError as e:\n",
+    "    print(f\"KeyError: {e}\")\n",
+    "    \n",
+    "    # Alternative approach: manually extract the data\n",
+    "    print(\"\\nTrying alternative approach to read the gene data:\")\n",
+    "    with gzip.open(matrix_file, 'rt') as file:\n",
+    "        # Find the start of the data\n",
+    "        for line in file:\n",
+    "            if '!series_matrix_table_begin' in line:\n",
+    "                break\n",
+    "                \n",
+    "        # Read the headers and data\n",
+    "        import pandas as pd\n",
+    "        df = pd.read_csv(file, sep='\\t', index_col=0)\n",
+    "        print(f\"Column names: {df.columns[:5]}\")\n",
+    "        print(f\"First 20 row IDs: {df.index[:20]}\")\n",
+    "        gene_data = df\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "50d83844",
+   "metadata": {},
+   "source": [
+    "### Step 4: Gene Identifier Review"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "59bd4ace",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2025-03-25T05:21:14.832916Z",
+     "iopub.status.busy": "2025-03-25T05:21:14.832801Z",
+     "iopub.status.idle": "2025-03-25T05:21:14.834703Z",
+     "shell.execute_reply": "2025-03-25T05:21:14.834418Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "# The gene identifiers appear to be numeric IDs (like \"16657439\")\n",
+    "# These are not standard human gene symbols, which would typically be names like \"BRCA1\", \"TP53\", etc.\n",
+    "# These look like probe IDs or transcript IDs that would need to be mapped to gene symbols\n",
+    "\n",
+    "requires_gene_mapping = True\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "50ced86d",
+   "metadata": {},
+   "source": [
+    "### Step 5: Gene Annotation"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "7a3c8d4d",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2025-03-25T05:21:14.835832Z",
+     "iopub.status.busy": "2025-03-25T05:21:14.835727Z",
+     "iopub.status.idle": "2025-03-25T05:21:17.409994Z",
+     "shell.execute_reply": "2025-03-25T05:21:17.409629Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Examining SOFT file structure:\n",
+      "Line 0: ^DATABASE = GeoMiame\n",
+      "Line 1: !Database_name = Gene Expression Omnibus (GEO)\n",
+      "Line 2: !Database_institute = NCBI NLM NIH\n",
+      "Line 3: !Database_web_link = http://www.ncbi.nlm.nih.gov/geo\n",
+      "Line 4: !Database_email = geo@ncbi.nlm.nih.gov\n",
+      "Line 5: ^SERIES = GSE129978\n",
+      "Line 6: !Series_title = AHR activation in glioblastoma cells and gene expression analysis of T cells in TCL1-AT mice.\n",
+      "Line 7: !Series_geo_accession = GSE129978\n",
+      "Line 8: !Series_status = Public on Aug 19 2020\n",
+      "Line 9: !Series_submission_date = Apr 17 2019\n",
+      "Line 10: !Series_last_update_date = Nov 18 2020\n",
+      "Line 11: !Series_pubmed_id = 32818467\n",
+      "Line 12: !Series_summary = This SuperSeries is composed of the SubSeries listed below.\n",
+      "Line 13: !Series_overall_design = Refer to individual Series\n",
+      "Line 14: !Series_type = Expression profiling by array\n",
+      "Line 15: !Series_sample_id = GSM3728779\n",
+      "Line 16: !Series_sample_id = GSM3728780\n",
+      "Line 17: !Series_sample_id = GSM3728781\n",
+      "Line 18: !Series_sample_id = GSM3728782\n",
+      "Line 19: !Series_sample_id = GSM3728783\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Gene annotation preview:\n",
+      "{'ID': ['17210850', '17210852', '17210855', '17210869', '17210883'], 'probeset_id': [17210850.0, 17210852.0, 17210855.0, 17210869.0, 17210883.0], 'SPOT_ID': ['chr1(+):3102016-3102125', 'chr1(+):3466587-3513553', 'chr1(+):4807823-4846739', 'chr1(+):4857694-4897909', 'chr1(+):4970857-4976820'], 'seqname': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'strand': ['+', '+', '+', '+', '+'], 'start': [3102016.0, 3466587.0, 4807823.0, 4857694.0, 4970857.0], 'stop': [3102125.0, 3513553.0, 4846739.0, 4897909.0, 4976820.0], 'total_probes': [8.0, 23.0, 20.0, 21.0, 23.0], 'gene_assignment': ['---', '---', 'NM_008866 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000027036 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// BC013536 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// BC052848 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// U89352 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// CT010201 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000134384 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000150971 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000134384 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000155020 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000141278 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK050549 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK167231 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000115529 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000137887 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK034851 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000131119 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000119612 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777', 'NM_001159751 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// ENSMUST00000165720 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// NM_011541 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// NM_001159750 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// ENSMUST00000081551 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// M18210 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399', '---'], 'mrna_assignment': ['ENSMUST00000082908 // ENSEMBL // ncrna:snRNA chromosome:NCBIM37:1:3092097:3092206:1 gene:ENSMUSG00000064842 gene_biotype:snRNA transcript_biotype:snRNA // chr1 // 100 // 100 // 8 // 8 // 0', 'ENSMUST00000161581 // ENSEMBL // cdna:putative chromosome:NCBIM37:1:3456668:3503634:1 gene:ENSMUSG00000089699 gene_biotype:antisense transcript_biotype:antisense // chr1 // 100 // 100 // 23 // 23 // 0', 'NM_008866 // RefSeq // Mus musculus lysophospholipase 1 (Lypla1), mRNA. // chr1 // 100 // 85 // 17 // 17 // 0 /// ENSMUST00000027036 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797904:4836820:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 85 // 17 // 17 // 0 /// BC013536 // GenBank // Mus musculus lysophospholipase 1, mRNA (cDNA clone MGC:19218 IMAGE:4240573), complete cds. // chr1 // 100 // 85 // 17 // 17 // 0 /// BC052848 // GenBank // Mus musculus lysophospholipase 1, mRNA (cDNA clone MGC:60679 IMAGE:30055025), complete cds. // chr1 // 94 // 85 // 16 // 17 // 0 /// U89352 // GenBank // Mus musculus lysophospholipase I mRNA, complete cds. // chr1 // 100 // 75 // 15 // 15 // 0 /// CT010201 // GenBank // Mus musculus full open reading frame cDNA clone RZPDo836F0950D for gene Lypla1, Lysophospholipase 1; complete cds, incl. stopcodon. // chr1 // 100 // 70 // 14 // 14 // 0 /// ENSMUST00000134384 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797869:4838491:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay // chr1 // 100 // 100 // 36 // 36 // 0 /// ENSMUST00000150971 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797999:4831367:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:retained_intron // chr1 // 100 // 70 // 14 // 14 // 0 /// ENSMUST00000134384 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797869:4838491:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay // chr1 // 100 // 60 // 12 // 12 // 0 /// ENSMUST00000155020 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797973:4876851:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay // chr1 // 100 // 60 // 12 // 12 // 0 /// ENSMUST00000141278 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4826986:4832908:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:retained_intron // chr1 // 100 // 25 // 5 // 5 // 0 /// AK050549 // GenBank HTC // Mus musculus adult pancreas islet cells cDNA, RIKEN full-length enriched library, clone:C820014D19 product:lysophospholipase 1, full insert sequence. // chr1 // 100 // 70 // 14 // 14 // 0 /// AK167231 // GenBank HTC // Mus musculus blastocyst blastocyst cDNA, RIKEN full-length enriched library, clone:I1C0043L13 product:lysophospholipase 1, full insert sequence. // chr1 // 100 // 70 // 14 // 14 // 0 /// ENSMUST00000115529 // ENSEMBL // cdna:novel chromosome:NCBIM37:1:4797992:4835433:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 65 // 13 // 13 // 0 /// ENSMUST00000137887 // ENSEMBL // cdna:novel chromosome:NCBIM37:1:4797979:4831050:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 55 // 11 // 11 // 0 /// AK034851 // GenBank HTC // Mus musculus 12 days embryo embryonic body between diaphragm region and neck cDNA, RIKEN full-length enriched library, clone:9430047N20 product:lysophospholipase 1, full insert sequence. // chr1 // 100 // 25 // 5 // 5 // 0 /// ENSMUST00000131119 // ENSEMBL // cdna:putative chromosome:NCBIM37:1:4798318:4831174:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 75 // 15 // 15 // 0 /// ENSMUST00000119612 // ENSEMBL // cdna:putative chromosome:NCBIM37:1:4797977:4835255:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:processed_transcript // chr1 // 100 // 50 // 10 // 10 // 0 /// GENSCAN00000010943 // ENSEMBL // cdna:genscan chromosome:NCBIM37:1:4803477:4844373:1 transcript_biotype:protein_coding // chr1 // 100 // 25 // 5 // 5 // 0', 'NM_001159751 // RefSeq // Mus musculus transcription elongation factor A (SII) 1 (Tcea1), transcript variant 1, mRNA. // chr1 // 100 // 81 // 17 // 17 // 0 /// ENSMUST00000165720 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4848409:4887987:1 gene:ENSMUSG00000033813 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 81 // 17 // 17 // 0 /// NM_011541 // RefSeq // Mus musculus transcription elongation factor A (SII) 1 (Tcea1), transcript variant 2, mRNA. // chr1 // 100 // 76 // 16 // 16 // 0 /// NM_001159750 // RefSeq // Mus musculus transcription elongation factor A (SII) 1 (Tcea1), transcript variant 3, mRNA. // chr1 // 100 // 76 // 16 // 16 // 0 /// ENSMUST00000081551 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4847775:4887987:1 gene:ENSMUSG00000033813 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 76 // 16 // 16 // 0 /// M18210 // GenBank // Mouse transcription factor S-II, clone PSII-3. // chr1 // 100 // 67 // 14 // 14 // 0', 'ENSMUST00000144339 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4960938:4966901:1 gene:ENSMUSG00000085623 gene_biotype:antisense transcript_biotype:antisense // chr1 // 100 // 100 // 23 // 23 // 0'], 'swissprot': ['---', '---', 'NM_008866 // P97823 /// BC013536 // P97823 /// BC052848 // P97823 /// U89352 // P97823 /// CT010201 // Q4FK51 /// CT010201 // P97823 /// AK050549 // P97823 /// AK167231 // P97823', 'NM_011541 // Q3UPE0 /// NM_011541 // Q3UWX7 /// NM_011541 // P10711 /// NM_001159750 // Q3UPE0 /// NM_001159750 // Q3UWX7 /// NM_001159750 // P10711 /// M18210 // P10711', '---'], 'unigene': ['---', '---', 'NM_008866 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000027036 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// BC013536 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// BC052848 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// U89352 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// CT010201 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000134384 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000150971 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000134384 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000155020 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000141278 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// AK050549 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// AK167231 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000115529 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000137887 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// AK034851 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000131119 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000119612 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult', 'NM_001159751 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000165720 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// NM_011541 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// NM_001159750 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000081551 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// M18210 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult', '---'], 'GO_biological_process': ['---', '---', 'NM_008866 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// NM_008866 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000027036 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000027036 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// BC013536 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// BC013536 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// BC052848 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// BC052848 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// U89352 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// U89352 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// CT010201 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// CT010201 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000150971 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000150971 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000155020 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000155020 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000141278 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000141278 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// AK050549 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// AK050549 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// AK167231 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// AK167231 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000115529 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000115529 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000137887 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000137887 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// AK034851 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// AK034851 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000131119 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000131119 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000119612 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000119612 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation', 'NM_001159751 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// NM_001159751 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// NM_001159751 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// NM_001159751 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// NM_001159751 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// NM_001159751 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// NM_001159751 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// ENSMUST00000165720 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// ENSMUST00000165720 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// ENSMUST00000165720 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// NM_011541 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// NM_011541 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// NM_011541 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// NM_011541 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// NM_011541 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// NM_011541 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// NM_011541 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// NM_001159750 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// NM_001159750 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// NM_001159750 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// NM_001159750 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// NM_001159750 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// NM_001159750 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// NM_001159750 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// ENSMUST00000081551 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// ENSMUST00000081551 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// ENSMUST00000081551 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// M18210 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// M18210 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// M18210 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// M18210 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// M18210 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// M18210 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// M18210 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay', '---'], 'GO_cellular_component': ['---', '---', 'NM_008866 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// NM_008866 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000027036 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000027036 // GO:0005739 // mitochondrion // inferred from direct assay  /// BC013536 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// BC013536 // GO:0005739 // mitochondrion // inferred from direct assay  /// BC052848 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// BC052848 // GO:0005739 // mitochondrion // inferred from direct assay  /// U89352 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// U89352 // GO:0005739 // mitochondrion // inferred from direct assay  /// CT010201 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// CT010201 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000134384 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000150971 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000150971 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000134384 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000155020 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000155020 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000141278 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000141278 // GO:0005739 // mitochondrion // inferred from direct assay  /// AK050549 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// AK050549 // GO:0005739 // mitochondrion // inferred from direct assay  /// AK167231 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// AK167231 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000115529 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000115529 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000137887 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000137887 // GO:0005739 // mitochondrion // inferred from direct assay  /// AK034851 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// AK034851 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000131119 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000131119 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000119612 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000119612 // GO:0005739 // mitochondrion // inferred from direct assay', 'NM_001159751 // GO:0005634 // nucleus // not recorded  /// NM_001159751 // GO:0005654 // nucleoplasm // inferred from direct assay  /// NM_001159751 // GO:0005730 // nucleolus // not recorded  /// ENSMUST00000165720 // GO:0005634 // nucleus // not recorded  /// ENSMUST00000165720 // GO:0005654 // nucleoplasm // inferred from direct assay  /// ENSMUST00000165720 // GO:0005730 // nucleolus // not recorded  /// NM_011541 // GO:0005634 // nucleus // not recorded  /// NM_011541 // GO:0005654 // nucleoplasm // inferred from direct assay  /// NM_011541 // GO:0005730 // nucleolus // not recorded  /// NM_001159750 // GO:0005634 // nucleus // not recorded  /// NM_001159750 // GO:0005654 // nucleoplasm // inferred from direct assay  /// NM_001159750 // GO:0005730 // nucleolus // not recorded  /// ENSMUST00000081551 // GO:0005634 // nucleus // not recorded  /// ENSMUST00000081551 // GO:0005654 // nucleoplasm // inferred from direct assay  /// ENSMUST00000081551 // GO:0005730 // nucleolus // not recorded  /// M18210 // GO:0005634 // nucleus // not recorded  /// M18210 // GO:0005654 // nucleoplasm // inferred from direct assay  /// M18210 // GO:0005730 // nucleolus // not recorded', '---'], 'GO_molecular_function': ['---', '---', 'NM_008866 // GO:0004622 // lysophospholipase activity // not recorded  /// NM_008866 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// NM_008866 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000027036 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000027036 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000027036 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// BC013536 // GO:0004622 // lysophospholipase activity // not recorded  /// BC013536 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// BC013536 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// BC052848 // GO:0004622 // lysophospholipase activity // not recorded  /// BC052848 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// BC052848 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// U89352 // GO:0004622 // lysophospholipase activity // not recorded  /// U89352 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// U89352 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// CT010201 // GO:0004622 // lysophospholipase activity // not recorded  /// CT010201 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// CT010201 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000134384 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000134384 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000150971 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000150971 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000150971 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000134384 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000134384 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000155020 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000155020 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000155020 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000141278 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000141278 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000141278 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// AK050549 // GO:0004622 // lysophospholipase activity // not recorded  /// AK050549 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// AK050549 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// AK167231 // GO:0004622 // lysophospholipase activity // not recorded  /// AK167231 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// AK167231 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000115529 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000115529 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000115529 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000137887 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000137887 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000137887 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// AK034851 // GO:0004622 // lysophospholipase activity // not recorded  /// AK034851 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// AK034851 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000131119 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000131119 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000131119 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000119612 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000119612 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000119612 // GO:0016787 // hydrolase activity // inferred from electronic annotation', 'NM_001159751 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// NM_001159751 // GO:0003677 // DNA binding // inferred from electronic annotation  /// NM_001159751 // GO:0005515 // protein binding // inferred from physical interaction  /// NM_001159751 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// NM_001159751 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0003677 // DNA binding // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0005515 // protein binding // inferred from physical interaction  /// ENSMUST00000165720 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// NM_011541 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// NM_011541 // GO:0003677 // DNA binding // inferred from electronic annotation  /// NM_011541 // GO:0005515 // protein binding // inferred from physical interaction  /// NM_011541 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// NM_011541 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// NM_001159750 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// NM_001159750 // GO:0003677 // DNA binding // inferred from electronic annotation  /// NM_001159750 // GO:0005515 // protein binding // inferred from physical interaction  /// NM_001159750 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// NM_001159750 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0003677 // DNA binding // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0005515 // protein binding // inferred from physical interaction  /// ENSMUST00000081551 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// M18210 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// M18210 // GO:0003677 // DNA binding // inferred from electronic annotation  /// M18210 // GO:0005515 // protein binding // inferred from physical interaction  /// M18210 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// M18210 // GO:0046872 // metal ion binding // inferred from electronic annotation', '---'], 'pathway': ['---', '---', '---', '---', '---'], 'protein_domains': ['---', '---', 'ENSMUST00000027036 // Pfam // IPR003140 // Phospholipase/carboxylesterase/thioesterase /// ENSMUST00000027036 // Pfam // IPR013094 // Alpha/beta hydrolase fold-3 /// ENSMUST00000115529 // Pfam // IPR003140 // Phospholipase/carboxylesterase/thioesterase /// ENSMUST00000137887 // Pfam // IPR003140 // Phospholipase/carboxylesterase/thioesterase /// ENSMUST00000137887 // Pfam // IPR013094 // Alpha/beta hydrolase fold-3 /// ENSMUST00000131119 // Pfam // IPR003140 // Phospholipase/carboxylesterase/thioesterase /// ENSMUST00000131119 // Pfam // IPR013094 // Alpha/beta hydrolase fold-3', 'ENSMUST00000165720 // Pfam // IPR001222 // Zinc finger, TFIIS-type /// ENSMUST00000165720 // Pfam // IPR003618 // Transcription elongation factor S-II, central domain /// ENSMUST00000165720 // Pfam // IPR017923 // Transcription factor IIS, N-terminal /// ENSMUST00000081551 // Pfam // IPR001222 // Zinc finger, TFIIS-type /// ENSMUST00000081551 // Pfam // IPR003618 // Transcription elongation factor S-II, central domain /// ENSMUST00000081551 // Pfam // IPR017923 // Transcription factor IIS, N-terminal', '---'], 'crosshyb_type': ['3', '1', '1', '1', '1'], 'category': ['main', 'main', 'main', 'main', 'main']}\n"
+     ]
+    }
+   ],
+   "source": [
+    "# 1. Let's first examine the structure of the SOFT file before trying to parse it\n",
+    "import gzip\n",
+    "\n",
+    "# Look at the first few lines of the SOFT file to understand its structure\n",
+    "print(\"Examining SOFT file structure:\")\n",
+    "try:\n",
+    "    with gzip.open(soft_file, 'rt') as file:\n",
+    "        # Read first 20 lines to understand the file structure\n",
+    "        for i, line in enumerate(file):\n",
+    "            if i < 20:\n",
+    "                print(f\"Line {i}: {line.strip()}\")\n",
+    "            else:\n",
+    "                break\n",
+    "except Exception as e:\n",
+    "    print(f\"Error reading SOFT file: {e}\")\n",
+    "\n",
+    "# 2. Now let's try a more robust approach to extract the gene annotation\n",
+    "# Instead of using the library function which failed, we'll implement a custom approach\n",
+    "try:\n",
+    "    # First, look for the platform section which contains gene annotation\n",
+    "    platform_data = []\n",
+    "    with gzip.open(soft_file, 'rt') as file:\n",
+    "        in_platform_section = False\n",
+    "        for line in file:\n",
+    "            if line.startswith('^PLATFORM'):\n",
+    "                in_platform_section = True\n",
+    "                continue\n",
+    "            if in_platform_section and line.startswith('!platform_table_begin'):\n",
+    "                # Next line should be the header\n",
+    "                header = next(file).strip()\n",
+    "                platform_data.append(header)\n",
+    "                # Read until the end of the platform table\n",
+    "                for table_line in file:\n",
+    "                    if table_line.startswith('!platform_table_end'):\n",
+    "                        break\n",
+    "                    platform_data.append(table_line.strip())\n",
+    "                break\n",
+    "    \n",
+    "    # If we found platform data, convert it to a DataFrame\n",
+    "    if platform_data:\n",
+    "        import pandas as pd\n",
+    "        import io\n",
+    "        platform_text = '\\n'.join(platform_data)\n",
+    "        gene_annotation = pd.read_csv(io.StringIO(platform_text), delimiter='\\t', \n",
+    "                                      low_memory=False, on_bad_lines='skip')\n",
+    "        print(\"\\nGene annotation preview:\")\n",
+    "        print(preview_df(gene_annotation))\n",
+    "    else:\n",
+    "        print(\"Could not find platform table in SOFT file\")\n",
+    "        \n",
+    "        # Try an alternative approach - extract mapping from other sections\n",
+    "        with gzip.open(soft_file, 'rt') as file:\n",
+    "            for line in file:\n",
+    "                if 'ANNOTATION information' in line or 'annotation information' in line:\n",
+    "                    print(f\"Found annotation information: {line.strip()}\")\n",
+    "                if line.startswith('!Platform_title') or line.startswith('!platform_title'):\n",
+    "                    print(f\"Platform title: {line.strip()}\")\n",
+    "            \n",
+    "except Exception as e:\n",
+    "    print(f\"Error processing gene annotation: {e}\")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "88be3111",
+   "metadata": {},
+   "source": [
+    "### Step 6: Gene Identifier Mapping"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "177e85b2",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2025-03-25T05:21:17.411834Z",
+     "iopub.status.busy": "2025-03-25T05:21:17.411727Z",
+     "iopub.status.idle": "2025-03-25T05:21:20.310908Z",
+     "shell.execute_reply": "2025-03-25T05:21:20.310274Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Platform ID found: GPL16570\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Platform annotation preview:\n",
+      "{'ID': ['17210850', '17210852', '17210855', '17210869', '17210883'], 'probeset_id': [17210850.0, 17210852.0, 17210855.0, 17210869.0, 17210883.0], 'SPOT_ID': ['chr1(+):3102016-3102125', 'chr1(+):3466587-3513553', 'chr1(+):4807823-4846739', 'chr1(+):4857694-4897909', 'chr1(+):4970857-4976820'], 'seqname': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'strand': ['+', '+', '+', '+', '+'], 'start': [3102016.0, 3466587.0, 4807823.0, 4857694.0, 4970857.0], 'stop': [3102125.0, 3513553.0, 4846739.0, 4897909.0, 4976820.0], 'total_probes': [8.0, 23.0, 20.0, 21.0, 23.0], 'gene_assignment': ['---', '---', 'NM_008866 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000027036 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// BC013536 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// BC052848 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// U89352 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// CT010201 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000134384 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000150971 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000134384 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000155020 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000141278 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK050549 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK167231 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000115529 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000137887 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK034851 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000131119 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000119612 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777', 'NM_001159751 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// ENSMUST00000165720 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// NM_011541 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// NM_001159750 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// ENSMUST00000081551 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// M18210 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399', '---'], 'mrna_assignment': ['ENSMUST00000082908 // ENSEMBL // ncrna:snRNA chromosome:NCBIM37:1:3092097:3092206:1 gene:ENSMUSG00000064842 gene_biotype:snRNA transcript_biotype:snRNA // chr1 // 100 // 100 // 8 // 8 // 0', 'ENSMUST00000161581 // ENSEMBL // cdna:putative chromosome:NCBIM37:1:3456668:3503634:1 gene:ENSMUSG00000089699 gene_biotype:antisense transcript_biotype:antisense // chr1 // 100 // 100 // 23 // 23 // 0', 'NM_008866 // RefSeq // Mus musculus lysophospholipase 1 (Lypla1), mRNA. // chr1 // 100 // 85 // 17 // 17 // 0 /// ENSMUST00000027036 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797904:4836820:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 85 // 17 // 17 // 0 /// BC013536 // GenBank // Mus musculus lysophospholipase 1, mRNA (cDNA clone MGC:19218 IMAGE:4240573), complete cds. // chr1 // 100 // 85 // 17 // 17 // 0 /// BC052848 // GenBank // Mus musculus lysophospholipase 1, mRNA (cDNA clone MGC:60679 IMAGE:30055025), complete cds. // chr1 // 94 // 85 // 16 // 17 // 0 /// U89352 // GenBank // Mus musculus lysophospholipase I mRNA, complete cds. // chr1 // 100 // 75 // 15 // 15 // 0 /// CT010201 // GenBank // Mus musculus full open reading frame cDNA clone RZPDo836F0950D for gene Lypla1, Lysophospholipase 1; complete cds, incl. stopcodon. // chr1 // 100 // 70 // 14 // 14 // 0 /// ENSMUST00000134384 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797869:4838491:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay // chr1 // 100 // 100 // 36 // 36 // 0 /// ENSMUST00000150971 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797999:4831367:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:retained_intron // chr1 // 100 // 70 // 14 // 14 // 0 /// ENSMUST00000134384 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797869:4838491:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay // chr1 // 100 // 60 // 12 // 12 // 0 /// ENSMUST00000155020 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4797973:4876851:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:nonsense_mediated_decay // chr1 // 100 // 60 // 12 // 12 // 0 /// ENSMUST00000141278 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4826986:4832908:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:retained_intron // chr1 // 100 // 25 // 5 // 5 // 0 /// AK050549 // GenBank HTC // Mus musculus adult pancreas islet cells cDNA, RIKEN full-length enriched library, clone:C820014D19 product:lysophospholipase 1, full insert sequence. // chr1 // 100 // 70 // 14 // 14 // 0 /// AK167231 // GenBank HTC // Mus musculus blastocyst blastocyst cDNA, RIKEN full-length enriched library, clone:I1C0043L13 product:lysophospholipase 1, full insert sequence. // chr1 // 100 // 70 // 14 // 14 // 0 /// ENSMUST00000115529 // ENSEMBL // cdna:novel chromosome:NCBIM37:1:4797992:4835433:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 65 // 13 // 13 // 0 /// ENSMUST00000137887 // ENSEMBL // cdna:novel chromosome:NCBIM37:1:4797979:4831050:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 55 // 11 // 11 // 0 /// AK034851 // GenBank HTC // Mus musculus 12 days embryo embryonic body between diaphragm region and neck cDNA, RIKEN full-length enriched library, clone:9430047N20 product:lysophospholipase 1, full insert sequence. // chr1 // 100 // 25 // 5 // 5 // 0 /// ENSMUST00000131119 // ENSEMBL // cdna:putative chromosome:NCBIM37:1:4798318:4831174:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 75 // 15 // 15 // 0 /// ENSMUST00000119612 // ENSEMBL // cdna:putative chromosome:NCBIM37:1:4797977:4835255:1 gene:ENSMUSG00000025903 gene_biotype:protein_coding transcript_biotype:processed_transcript // chr1 // 100 // 50 // 10 // 10 // 0 /// GENSCAN00000010943 // ENSEMBL // cdna:genscan chromosome:NCBIM37:1:4803477:4844373:1 transcript_biotype:protein_coding // chr1 // 100 // 25 // 5 // 5 // 0', 'NM_001159751 // RefSeq // Mus musculus transcription elongation factor A (SII) 1 (Tcea1), transcript variant 1, mRNA. // chr1 // 100 // 81 // 17 // 17 // 0 /// ENSMUST00000165720 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4848409:4887987:1 gene:ENSMUSG00000033813 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 81 // 17 // 17 // 0 /// NM_011541 // RefSeq // Mus musculus transcription elongation factor A (SII) 1 (Tcea1), transcript variant 2, mRNA. // chr1 // 100 // 76 // 16 // 16 // 0 /// NM_001159750 // RefSeq // Mus musculus transcription elongation factor A (SII) 1 (Tcea1), transcript variant 3, mRNA. // chr1 // 100 // 76 // 16 // 16 // 0 /// ENSMUST00000081551 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4847775:4887987:1 gene:ENSMUSG00000033813 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 76 // 16 // 16 // 0 /// M18210 // GenBank // Mouse transcription factor S-II, clone PSII-3. // chr1 // 100 // 67 // 14 // 14 // 0', 'ENSMUST00000144339 // ENSEMBL // cdna:known chromosome:NCBIM37:1:4960938:4966901:1 gene:ENSMUSG00000085623 gene_biotype:antisense transcript_biotype:antisense // chr1 // 100 // 100 // 23 // 23 // 0'], 'swissprot': ['---', '---', 'NM_008866 // P97823 /// BC013536 // P97823 /// BC052848 // P97823 /// U89352 // P97823 /// CT010201 // Q4FK51 /// CT010201 // P97823 /// AK050549 // P97823 /// AK167231 // P97823', 'NM_011541 // Q3UPE0 /// NM_011541 // Q3UWX7 /// NM_011541 // P10711 /// NM_001159750 // Q3UPE0 /// NM_001159750 // Q3UWX7 /// NM_001159750 // P10711 /// M18210 // P10711', '---'], 'unigene': ['---', '---', 'NM_008866 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000027036 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// BC013536 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// BC052848 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// U89352 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// CT010201 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000134384 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000150971 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000134384 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000155020 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000141278 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// AK050549 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// AK167231 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000115529 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000137887 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// AK034851 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000131119 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000119612 // Mm.299955 // bladder| blood| bone| bone marrow| brain| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| mammary gland| molar| ovary| pancreas| pituitary gland| salivary gland| skin| spleen| testis| thymus|oocyte| zygote| cleavage| morula| blastocyst| egg cylinder| gastrula| organogenesis| fetus| neonate| juvenile| adult', 'NM_001159751 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000165720 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// NM_011541 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// NM_001159750 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// ENSMUST00000081551 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult /// M18210 // Mm.207263 // blood| bone| bone marrow| brain| connective tissue| dorsal root ganglion| embryonic tissue| extraembryonic tissue| eye| fertilized ovum| heart| inner ear| intestine| kidney| liver| lung| lymph node| mammary gland| muscle| nasopharynx| ovary| pancreas| salivary gland| skin| spleen| sympathetic ganglion| testis| thymus| thyroid| tongue| uterus|oocyte| unfertilized ovum| zygote| cleavage| morula| blastocyst| gastrula| organogenesis| fetus| neonate| juvenile| adult', '---'], 'GO_biological_process': ['---', '---', 'NM_008866 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// NM_008866 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000027036 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000027036 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// BC013536 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// BC013536 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// BC052848 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// BC052848 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// U89352 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// U89352 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// CT010201 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// CT010201 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000150971 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000150971 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000155020 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000155020 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000141278 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000141278 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// AK050549 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// AK050549 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// AK167231 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// AK167231 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000115529 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000115529 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000137887 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000137887 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// AK034851 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// AK034851 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000131119 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000131119 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation  /// ENSMUST00000119612 // GO:0006629 // lipid metabolic process // inferred from electronic annotation  /// ENSMUST00000119612 // GO:0006631 // fatty acid metabolic process // inferred from electronic annotation', 'NM_001159751 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// NM_001159751 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// NM_001159751 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// NM_001159751 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// NM_001159751 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// NM_001159751 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// NM_001159751 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// ENSMUST00000165720 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// ENSMUST00000165720 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// ENSMUST00000165720 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// NM_011541 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// NM_011541 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// NM_011541 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// NM_011541 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// NM_011541 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// NM_011541 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// NM_011541 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// NM_001159750 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// NM_001159750 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// NM_001159750 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// NM_001159750 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// NM_001159750 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// NM_001159750 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// NM_001159750 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// ENSMUST00000081551 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// ENSMUST00000081551 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// ENSMUST00000081551 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay  /// M18210 // GO:0006351 // transcription, DNA-dependent // inferred from electronic annotation  /// M18210 // GO:0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation  /// M18210 // GO:0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation  /// M18210 // GO:0030218 // erythrocyte differentiation // inferred from mutant phenotype  /// M18210 // GO:0032784 // regulation of transcription elongation, DNA-dependent // inferred from electronic annotation  /// M18210 // GO:0045893 // positive regulation of transcription, DNA-dependent // inferred from direct assay  /// M18210 // GO:0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay', '---'], 'GO_cellular_component': ['---', '---', 'NM_008866 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// NM_008866 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000027036 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000027036 // GO:0005739 // mitochondrion // inferred from direct assay  /// BC013536 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// BC013536 // GO:0005739 // mitochondrion // inferred from direct assay  /// BC052848 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// BC052848 // GO:0005739 // mitochondrion // inferred from direct assay  /// U89352 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// U89352 // GO:0005739 // mitochondrion // inferred from direct assay  /// CT010201 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// CT010201 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000134384 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000150971 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000150971 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000134384 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000155020 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000155020 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000141278 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000141278 // GO:0005739 // mitochondrion // inferred from direct assay  /// AK050549 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// AK050549 // GO:0005739 // mitochondrion // inferred from direct assay  /// AK167231 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// AK167231 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000115529 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000115529 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000137887 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000137887 // GO:0005739 // mitochondrion // inferred from direct assay  /// AK034851 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// AK034851 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000131119 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000131119 // GO:0005739 // mitochondrion // inferred from direct assay  /// ENSMUST00000119612 // GO:0005737 // cytoplasm // inferred from electronic annotation  /// ENSMUST00000119612 // GO:0005739 // mitochondrion // inferred from direct assay', 'NM_001159751 // GO:0005634 // nucleus // not recorded  /// NM_001159751 // GO:0005654 // nucleoplasm // inferred from direct assay  /// NM_001159751 // GO:0005730 // nucleolus // not recorded  /// ENSMUST00000165720 // GO:0005634 // nucleus // not recorded  /// ENSMUST00000165720 // GO:0005654 // nucleoplasm // inferred from direct assay  /// ENSMUST00000165720 // GO:0005730 // nucleolus // not recorded  /// NM_011541 // GO:0005634 // nucleus // not recorded  /// NM_011541 // GO:0005654 // nucleoplasm // inferred from direct assay  /// NM_011541 // GO:0005730 // nucleolus // not recorded  /// NM_001159750 // GO:0005634 // nucleus // not recorded  /// NM_001159750 // GO:0005654 // nucleoplasm // inferred from direct assay  /// NM_001159750 // GO:0005730 // nucleolus // not recorded  /// ENSMUST00000081551 // GO:0005634 // nucleus // not recorded  /// ENSMUST00000081551 // GO:0005654 // nucleoplasm // inferred from direct assay  /// ENSMUST00000081551 // GO:0005730 // nucleolus // not recorded  /// M18210 // GO:0005634 // nucleus // not recorded  /// M18210 // GO:0005654 // nucleoplasm // inferred from direct assay  /// M18210 // GO:0005730 // nucleolus // not recorded', '---'], 'GO_molecular_function': ['---', '---', 'NM_008866 // GO:0004622 // lysophospholipase activity // not recorded  /// NM_008866 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// NM_008866 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000027036 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000027036 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000027036 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// BC013536 // GO:0004622 // lysophospholipase activity // not recorded  /// BC013536 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// BC013536 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// BC052848 // GO:0004622 // lysophospholipase activity // not recorded  /// BC052848 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// BC052848 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// U89352 // GO:0004622 // lysophospholipase activity // not recorded  /// U89352 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// U89352 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// CT010201 // GO:0004622 // lysophospholipase activity // not recorded  /// CT010201 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// CT010201 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000134384 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000134384 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000150971 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000150971 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000150971 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000134384 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000134384 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000134384 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000155020 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000155020 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000155020 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000141278 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000141278 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000141278 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// AK050549 // GO:0004622 // lysophospholipase activity // not recorded  /// AK050549 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// AK050549 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// AK167231 // GO:0004622 // lysophospholipase activity // not recorded  /// AK167231 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// AK167231 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000115529 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000115529 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000115529 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000137887 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000137887 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000137887 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// AK034851 // GO:0004622 // lysophospholipase activity // not recorded  /// AK034851 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// AK034851 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000131119 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000131119 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000131119 // GO:0016787 // hydrolase activity // inferred from electronic annotation  /// ENSMUST00000119612 // GO:0004622 // lysophospholipase activity // not recorded  /// ENSMUST00000119612 // GO:0008474 // palmitoyl-(protein) hydrolase activity // not recorded  /// ENSMUST00000119612 // GO:0016787 // hydrolase activity // inferred from electronic annotation', 'NM_001159751 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// NM_001159751 // GO:0003677 // DNA binding // inferred from electronic annotation  /// NM_001159751 // GO:0005515 // protein binding // inferred from physical interaction  /// NM_001159751 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// NM_001159751 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0003677 // DNA binding // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0005515 // protein binding // inferred from physical interaction  /// ENSMUST00000165720 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// ENSMUST00000165720 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// NM_011541 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// NM_011541 // GO:0003677 // DNA binding // inferred from electronic annotation  /// NM_011541 // GO:0005515 // protein binding // inferred from physical interaction  /// NM_011541 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// NM_011541 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// NM_001159750 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// NM_001159750 // GO:0003677 // DNA binding // inferred from electronic annotation  /// NM_001159750 // GO:0005515 // protein binding // inferred from physical interaction  /// NM_001159750 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// NM_001159750 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0003677 // DNA binding // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0005515 // protein binding // inferred from physical interaction  /// ENSMUST00000081551 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// ENSMUST00000081551 // GO:0046872 // metal ion binding // inferred from electronic annotation  /// M18210 // GO:0003676 // nucleic acid binding // inferred from electronic annotation  /// M18210 // GO:0003677 // DNA binding // inferred from electronic annotation  /// M18210 // GO:0005515 // protein binding // inferred from physical interaction  /// M18210 // GO:0008270 // zinc ion binding // inferred from electronic annotation  /// M18210 // GO:0046872 // metal ion binding // inferred from electronic annotation', '---'], 'pathway': ['---', '---', '---', '---', '---'], 'protein_domains': ['---', '---', 'ENSMUST00000027036 // Pfam // IPR003140 // Phospholipase/carboxylesterase/thioesterase /// ENSMUST00000027036 // Pfam // IPR013094 // Alpha/beta hydrolase fold-3 /// ENSMUST00000115529 // Pfam // IPR003140 // Phospholipase/carboxylesterase/thioesterase /// ENSMUST00000137887 // Pfam // IPR003140 // Phospholipase/carboxylesterase/thioesterase /// ENSMUST00000137887 // Pfam // IPR013094 // Alpha/beta hydrolase fold-3 /// ENSMUST00000131119 // Pfam // IPR003140 // Phospholipase/carboxylesterase/thioesterase /// ENSMUST00000131119 // Pfam // IPR013094 // Alpha/beta hydrolase fold-3', 'ENSMUST00000165720 // Pfam // IPR001222 // Zinc finger, TFIIS-type /// ENSMUST00000165720 // Pfam // IPR003618 // Transcription elongation factor S-II, central domain /// ENSMUST00000165720 // Pfam // IPR017923 // Transcription factor IIS, N-terminal /// ENSMUST00000081551 // Pfam // IPR001222 // Zinc finger, TFIIS-type /// ENSMUST00000081551 // Pfam // IPR003618 // Transcription elongation factor S-II, central domain /// ENSMUST00000081551 // Pfam // IPR017923 // Transcription factor IIS, N-terminal', '---'], 'crosshyb_type': ['3', '1', '1', '1', '1'], 'category': ['main', 'main', 'main', 'main', 'main']}\n",
+      "\n",
+      "Potential gene name columns: ['gene_assignment', 'mrna_assignment', 'unigene']\n",
+      "\n",
+      "Sample genes: ['---', '---', 'NM_008866 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000027036 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// BC013536 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// BC052848 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// U89352 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// CT010201 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000134384 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000150971 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000134384 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000155020 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000141278 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK050549 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK167231 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000115529 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000137887 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// AK034851 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000131119 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777 /// ENSMUST00000119612 // Lypla1 // lysophospholipase 1 // 1 A1|1 // 18777', 'NM_001159751 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// ENSMUST00000165720 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// NM_011541 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// NM_001159750 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// ENSMUST00000081551 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399 /// M18210 // Tcea1 // transcription elongation factor A (SII) 1 // 1 A1|1 // 21399', '---', 'NM_133826 // Atp6v1h // ATPase, H+ transporting, lysosomal V1 subunit H // 1 A1|1 // 108664 /// ENSMUST00000044369 // Atp6v1h // ATPase, H+ transporting, lysosomal V1 subunit H // 1 A1|1 // 108664 /// BC009154 // Atp6v1h // ATPase, H+ transporting, lysosomal V1 subunit H // 1 A1|1 // 108664', 'NM_001204371 // Oprk1 // opioid receptor, kappa 1 // 1 A2-A3|1 5.5 cM // 18387 /// NM_011011 // Oprk1 // opioid receptor, kappa 1 // 1 A2-A3|1 5.5 cM // 18387 /// ENSMUST00000160777 // Oprk1 // opioid receptor, kappa 1 // 1 A2-A3|1 5.5 cM // 18387 /// ENSMUST00000160339 // Oprk1 // opioid receptor, kappa 1 // 1 A2-A3|1 5.5 cM // 18387 /// ENSMUST00000027038 // Oprk1 // opioid receptor, kappa 1 // 1 A2-A3|1 5.5 cM // 18387 /// L11065 // Oprk1 // opioid receptor, kappa 1 // 1 A2-A3|1 5.5 cM // 18387 /// ENSMUST00000159083 // Oprk1 // opioid receptor, kappa 1 // 1 A2-A3|1 5.5 cM // 18387', 'ENSMUST00000027040 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// NM_009826 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// AB070619 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// AB050017 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// BC150774 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000167867 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000159906 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000160871 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000159802 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000162257 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000162210 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000160062 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000159661 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000159656 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000161327 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// AK165119 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// AK020027 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000162795 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421 /// ENSMUST00000159530 // Rb1cc1 // RB1-inducible coiled-coil 1 // 1|1 A2 // 12421', 'NM_001195732 // Fam150a // family with sequence similarity 150, member A // 1 A1|1 // 620393', 'NR_045188 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000043578 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// NM_001244692 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// NR_045189 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000140079 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000150761 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// NM_001244693 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// NM_173868 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000131494 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000163727 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000151281 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// BC118528 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000151015 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000126379 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000139756 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690 /// ENSMUST00000124167 // St18 // suppression of tumorigenicity 18 // 1 A1|1 // 240690']\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Number of common IDs between mapping and expression data: 27036\n",
+      "Sample of common IDs: ['17308796', '17269769', '17333375', '17520146', '17325874']\n",
+      "\n",
+      "Gene expression data shape: (412, 16)\n",
+      "First few gene symbols: ['A530046M15', 'A530065N20', 'A630020A06', 'A730015I17', 'A730034C02', 'A730043L09', 'A830025M08', 'A830049A06', 'A830060N17', 'AA066038']\n",
+      "Gene expression data saved to ../../output/preprocess/Glioblastoma/gene_data/GSE129978.csv\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Step 1: Let's examine the SOFT file more thoroughly to identify the correct platform\n",
+    "import gzip\n",
+    "import re\n",
+    "\n",
+    "# Look for platform information in the SOFT file\n",
+    "platform_id = None\n",
+    "with gzip.open(soft_file, 'rt') as file:\n",
+    "    for line in file:\n",
+    "        if line.startswith('!Series_platform_id'):\n",
+    "            platform_id = line.strip().split('=')[1].strip()\n",
+    "            print(f\"Platform ID found: {platform_id}\")\n",
+    "            break\n",
+    "\n",
+    "# Extract platform-specific annotation data\n",
+    "platform_data = []\n",
+    "in_platform_section = False\n",
+    "with gzip.open(soft_file, 'rt') as file:\n",
+    "    for line in file:\n",
+    "        if line.startswith(f'^PLATFORM = {platform_id}'):\n",
+    "            in_platform_section = True\n",
+    "            continue\n",
+    "        elif line.startswith('^') and in_platform_section:\n",
+    "            # We've moved to another section\n",
+    "            break\n",
+    "        elif in_platform_section and line.startswith('!platform_table_begin'):\n",
+    "            # Next line should be the header\n",
+    "            header = next(file).strip()\n",
+    "            platform_data.append(header)\n",
+    "            # Read until the end of the platform table\n",
+    "            for table_line in file:\n",
+    "                if table_line.startswith('!platform_table_end'):\n",
+    "                    break\n",
+    "                platform_data.append(table_line.strip())\n",
+    "            break\n",
+    "\n",
+    "# If we found platform data, convert it to a DataFrame\n",
+    "if platform_data:\n",
+    "    import pandas as pd\n",
+    "    import io\n",
+    "    platform_text = '\\n'.join(platform_data)\n",
+    "    platform_annotation = pd.read_csv(io.StringIO(platform_text), delimiter='\\t', \n",
+    "                                     low_memory=False, on_bad_lines='skip')\n",
+    "    print(\"\\nPlatform annotation preview:\")\n",
+    "    print(preview_df(platform_annotation))\n",
+    "    \n",
+    "    # Extract ID and gene columns\n",
+    "    id_col = 'ID' if 'ID' in platform_annotation.columns else platform_annotation.columns[0]\n",
+    "    \n",
+    "    # Check potential gene name columns\n",
+    "    potential_gene_cols = [col for col in platform_annotation.columns \n",
+    "                          if any(term in col.lower() for term in ['gene', 'symbol', 'mrna'])]\n",
+    "    print(f\"\\nPotential gene name columns: {potential_gene_cols}\")\n",
+    "    \n",
+    "    if potential_gene_cols:\n",
+    "        gene_col = potential_gene_cols[0]\n",
+    "        # Create mapping dataframe\n",
+    "        mapping_df = platform_annotation[[id_col, gene_col]].copy()\n",
+    "        mapping_df = mapping_df.rename(columns={id_col: 'ID', gene_col: 'Gene'})\n",
+    "        mapping_df['ID'] = mapping_df['ID'].astype(str)\n",
+    "        mapping_df = mapping_df.dropna()\n",
+    "        \n",
+    "        # Check for gene symbols\n",
+    "        is_gene_symbols = True\n",
+    "        sample_genes = mapping_df['Gene'].dropna().head(10).tolist()\n",
+    "        if len(sample_genes) > 0:\n",
+    "            print(f\"\\nSample genes: {sample_genes}\")\n",
+    "            # Check if we need to extract symbols\n",
+    "            if any('/' in str(gene) or '//' in str(gene) for gene in sample_genes):\n",
+    "                is_gene_symbols = False\n",
+    "        \n",
+    "        # If not direct gene symbols, extract them\n",
+    "        if not is_gene_symbols:\n",
+    "            # Use the mouse gene extraction function\n",
+    "            def extract_mouse_gene_symbols(text):\n",
+    "                \"\"\"Extract mouse gene symbols from gene_assignment text\"\"\"\n",
+    "                if not isinstance(text, str):\n",
+    "                    return []\n",
+    "                \n",
+    "                # Extract gene symbols after \"//\" pattern\n",
+    "                symbols = []\n",
+    "                matches = re.findall(r'[A-Z]+\\d+_\\d+ // ([A-Za-z0-9-]+) //', text)\n",
+    "                if matches:\n",
+    "                    symbols.extend(matches)\n",
+    "                \n",
+    "                # If no matches found, try a more general pattern\n",
+    "                if not symbols:\n",
+    "                    matches = re.findall(r'// ([A-Za-z0-9][A-Za-z0-9-]{1,20}) //', text)\n",
+    "                    if matches:\n",
+    "                        symbols.extend(matches)\n",
+    "                \n",
+    "                return list(dict.fromkeys(symbols))\n",
+    "            \n",
+    "            mapping_df['Gene'] = mapping_df['Gene'].apply(extract_mouse_gene_symbols)\n",
+    "            mapping_df = mapping_df.explode('Gene').dropna(subset=['Gene'])\n",
+    "    else:\n",
+    "        # If no obvious gene column, try to extract from description or another field\n",
+    "        desc_col = next((col for col in platform_annotation.columns \n",
+    "                        if any(term in col.lower() for term in ['desc', 'definition', 'assignment'])), None)\n",
+    "        \n",
+    "        if desc_col:\n",
+    "            mapping_df = platform_annotation[[id_col, desc_col]].copy()\n",
+    "            mapping_df = mapping_df.rename(columns={id_col: 'ID', desc_col: 'Gene'})\n",
+    "            mapping_df['ID'] = mapping_df['ID'].astype(str)\n",
+    "            mapping_df = mapping_df.dropna()\n",
+    "            \n",
+    "            # Extract gene symbols\n",
+    "            mapping_df['Gene'] = mapping_df['Gene'].apply(extract_human_gene_symbols)\n",
+    "            # Explode the list of genes into separate rows\n",
+    "            mapping_df = mapping_df.explode('Gene').dropna(subset=['Gene'])\n",
+    "        else:\n",
+    "            # If we can't find any gene annotation, we'll have to skip the mapping\n",
+    "            mapping_df = None\n",
+    "\n",
+    "# Check if any IDs in mapping_df match gene_data index\n",
+    "if mapping_df is not None:\n",
+    "    common_ids = set(mapping_df['ID']).intersection(set(gene_data.index))\n",
+    "    print(f\"\\nNumber of common IDs between mapping and expression data: {len(common_ids)}\")\n",
+    "    print(f\"Sample of common IDs: {list(common_ids)[:5]}\")\n",
+    "    \n",
+    "    # Apply gene mapping only if there are common IDs\n",
+    "    if common_ids:\n",
+    "        # Drop Gene column if it already exists\n",
+    "        if 'Gene' in gene_data.columns:\n",
+    "            gene_data = gene_data.drop(columns=['Gene'])\n",
+    "            \n",
+    "        # Apply the mapping\n",
+    "        gene_data = apply_gene_mapping(gene_data, mapping_df)\n",
+    "        \n",
+    "        # Preview the gene expression data\n",
+    "        print(f\"\\nGene expression data shape: {gene_data.shape}\")\n",
+    "        print(f\"First few gene symbols: {gene_data.index[:10].tolist()}\")\n",
+    "    else:\n",
+    "        print(\"\\nNo matching probe IDs found between annotation and expression data.\")\n",
+    "        # In this case, we can't map to gene symbols, so we'll use probe IDs as is\n",
+    "        gene_data = gene_data.copy()\n",
+    "        print(f\"Using probe IDs directly. Shape: {gene_data.shape}\")\n",
+    "else:\n",
+    "    print(\"\\nCould not find suitable gene annotation data\")\n",
+    "    # Use probe IDs directly\n",
+    "    gene_data = gene_data.copy()\n",
+    "\n",
+    "# Save the gene expression data\n",
+    "os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)\n",
+    "gene_data.to_csv(out_gene_data_file)\n",
+    "print(f\"Gene expression data saved to {out_gene_data_file}\")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0bb17ccb",
+   "metadata": {},
+   "source": [
+    "### Step 7: Data Normalization and Linking"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "ff6b6a3f",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2025-03-25T05:21:20.312343Z",
+     "iopub.status.busy": "2025-03-25T05:21:20.312225Z",
+     "iopub.status.idle": "2025-03-25T05:21:20.410857Z",
+     "shell.execute_reply": "2025-03-25T05:21:20.410335Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Gene data shape after normalization: (33, 16)\n",
+      "Sample gene symbols after normalization: ['ATP6', 'ATP8', 'C2', 'C3', 'C6', 'C7', 'C9', 'COX1', 'COX2', 'COX3']\n",
+      "Gene data saved to ../../output/preprocess/Glioblastoma/gene_data/GSE129978.csv\n",
+      "Clinical data shape: (1, 16)\n",
+      "Clinical data preview:\n",
+      "              GSM4514184  GSM4514185  GSM4514186  GSM4514187  GSM4514188\n",
+      "Glioblastoma           1           1           1           1           1\n",
+      "Clinical data saved to ../../output/preprocess/Glioblastoma/clinical_data/GSE129978.csv\n",
+      "Linked data shape: (16, 34)\n",
+      "Linked data preview (first 5 rows, first 5 columns):\n",
+      "            Glioblastoma     ATP6     ATP8      C2      C3\n",
+      "GSM4514184           1.0  10.7716  10.7716  3.2225  4.6422\n",
+      "GSM4514185           1.0  10.6608  10.6608  3.1908  5.4308\n",
+      "GSM4514186           1.0  10.6187  10.6187  3.0901  4.9176\n",
+      "GSM4514187           1.0  11.1555  11.1555  2.5386  3.9111\n",
+      "GSM4514188           1.0  10.8219  10.8219  3.1858  5.7965\n",
+      "\n",
+      "Missing values before handling:\n",
+      "  Trait (Glioblastoma) missing: 0 out of 16\n",
+      "  Genes with >20% missing: 0\n",
+      "  Samples with >5% missing genes: 0\n",
+      "Data shape after handling missing values: (16, 34)\n",
+      "The feature 'Glioblastoma' is biased - all samples have the same value.\n",
+      "A new JSON file was created at: ../../output/preprocess/Glioblastoma/cohort_info.json\n",
+      "Data was determined to be unusable or empty and was not saved\n"
+     ]
+    }
+   ],
+   "source": [
+    "# 1. Examine gene_data to decide on the right approach\n",
+    "# We need to check if we're dealing with gene symbols or just probe IDs\n",
+    "has_gene_symbols = False\n",
+    "if isinstance(gene_data.index[0], str) and any(c.isalpha() for c in gene_data.index[0]):\n",
+    "    # Check if index contains alphabetic characters, suggesting gene symbols\n",
+    "    has_gene_symbols = True\n",
+    "\n",
+    "# Only normalize if we have gene symbols\n",
+    "if has_gene_symbols:\n",
+    "    normalized_gene_data = normalize_gene_symbols_in_index(gene_data)\n",
+    "    print(f\"Gene data shape after normalization: {normalized_gene_data.shape}\")\n",
+    "    print(f\"Sample gene symbols after normalization: {list(normalized_gene_data.index[:10])}\")\n",
+    "else:\n",
+    "    # If no gene symbols, just use probe IDs directly\n",
+    "    normalized_gene_data = gene_data.copy()\n",
+    "    print(f\"Using probe IDs directly. Gene data shape: {normalized_gene_data.shape}\")\n",
+    "    print(f\"Sample probe IDs: {list(normalized_gene_data.index[:10])}\")\n",
+    "\n",
+    "# Save the gene data\n",
+    "os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)\n",
+    "normalized_gene_data.to_csv(out_gene_data_file)\n",
+    "print(f\"Gene data saved to {out_gene_data_file}\")\n",
+    "\n",
+    "# 2. Generate clinical data - all samples are glioblastoma cell lines\n",
+    "# Create a proper clinical dataframe with trait information\n",
+    "clinical_df = pd.DataFrame(index=[trait], \n",
+    "                          data={col: 1 for col in normalized_gene_data.columns})\n",
+    "print(f\"Clinical data shape: {clinical_df.shape}\")\n",
+    "print(\"Clinical data preview:\")\n",
+    "print(clinical_df.iloc[:, :5])  # Show first 5 columns only\n",
+    "\n",
+    "# Save the clinical features\n",
+    "os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n",
+    "clinical_df.to_csv(out_clinical_data_file)\n",
+    "print(f\"Clinical data saved to {out_clinical_data_file}\")\n",
+    "\n",
+    "# 3. Link clinical and genetic data\n",
+    "linked_data = geo_link_clinical_genetic_data(clinical_df, normalized_gene_data)\n",
+    "print(f\"Linked data shape: {linked_data.shape}\")\n",
+    "print(\"Linked data preview (first 5 rows, first 5 columns):\")\n",
+    "if linked_data.shape[1] >= 5:\n",
+    "    print(linked_data.iloc[:5, :5])\n",
+    "else:\n",
+    "    print(linked_data.head())\n",
+    "\n",
+    "# 4. Handle missing values\n",
+    "print(\"\\nMissing values before handling:\")\n",
+    "print(f\"  Trait ({trait}) missing: {linked_data[trait].isna().sum()} out of {len(linked_data)}\")\n",
+    "gene_cols = [col for col in linked_data.columns if col != trait]\n",
+    "if gene_cols:\n",
+    "    missing_genes_pct = linked_data[gene_cols].isna().mean()\n",
+    "    genes_with_high_missing = sum(missing_genes_pct > 0.2)\n",
+    "    print(f\"  Genes with >20% missing: {genes_with_high_missing}\")\n",
+    "    \n",
+    "    if len(linked_data) > 0:  # Ensure we have samples before checking\n",
+    "        missing_per_sample = linked_data[gene_cols].isna().mean(axis=1)\n",
+    "        samples_with_high_missing = sum(missing_per_sample > 0.05)\n",
+    "        print(f\"  Samples with >5% missing genes: {samples_with_high_missing}\")\n",
+    "\n",
+    "# Only proceed with missing value handling if we have gene data\n",
+    "if len(gene_cols) > 0:\n",
+    "    cleaned_data = handle_missing_values(linked_data, trait)\n",
+    "    print(f\"Data shape after handling missing values: {cleaned_data.shape}\")\n",
+    "else:\n",
+    "    # If we only have trait data, we can't do much analysis\n",
+    "    cleaned_data = linked_data.copy()\n",
+    "    print(\"No gene data available for missing value handling.\")\n",
+    "\n",
+    "# 5. Evaluate bias in trait and demographic features\n",
+    "is_trait_biased = False\n",
+    "if len(cleaned_data) > 0:\n",
+    "    # If all samples have same trait value, it's biased\n",
+    "    if cleaned_data[trait].nunique() <= 1:\n",
+    "        is_trait_biased = True\n",
+    "        print(f\"The feature '{trait}' is biased - all samples have the same value.\")\n",
+    "    else:\n",
+    "        trait_biased, cleaned_data = judge_and_remove_biased_features(cleaned_data, trait)\n",
+    "        is_trait_biased = trait_biased\n",
+    "else:\n",
+    "    print(\"No data remains after handling missing values.\")\n",
+    "    is_trait_biased = True\n",
+    "\n",
+    "# 6. Final validation and save\n",
+    "note = \"Dataset contains gene expression data from glioblastoma cell lines. \"\n",
+    "note += \"No demographic features available. \" \n",
+    "if len(gene_cols) == 0:\n",
+    "    note += \"No usable gene measurements after processing.\"\n",
+    "\n",
+    "is_gene_available = len(normalized_gene_data) > 0 and len(gene_cols) > 0\n",
+    "is_usable = validate_and_save_cohort_info(\n",
+    "    is_final=True, \n",
+    "    cohort=cohort, \n",
+    "    info_path=json_path, \n",
+    "    is_gene_available=is_gene_available, \n",
+    "    is_trait_available=True, \n",
+    "    is_biased=is_trait_biased, \n",
+    "    df=cleaned_data,\n",
+    "    note=note\n",
+    ")\n",
+    "\n",
+    "# 7. Save if usable\n",
+    "if is_usable and len(cleaned_data) > 0:\n",
+    "    os.makedirs(os.path.dirname(out_data_file), exist_ok=True)\n",
+    "    cleaned_data.to_csv(out_data_file)\n",
+    "    print(f\"Linked data saved to {out_data_file}\")\n",
+    "else:\n",
+    "    print(\"Data was determined to be unusable or empty and was not saved\")"
+   ]
+  }
+ ],
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