{
 "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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