{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "50be79f8", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:41:33.501453Z", "iopub.status.busy": "2025-03-25T03:41:33.501339Z", "iopub.status.idle": "2025-03-25T03:41:33.670483Z", "shell.execute_reply": "2025-03-25T03:41:33.670124Z" } }, "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 = \"Psoriasis\"\n", "cohort = \"GSE158448\"\n", "\n", "# Input paths\n", "in_trait_dir = \"../../input/GEO/Psoriasis\"\n", "in_cohort_dir = \"../../input/GEO/Psoriasis/GSE158448\"\n", "\n", "# Output paths\n", "out_data_file = \"../../output/preprocess/Psoriasis/GSE158448.csv\"\n", "out_gene_data_file = \"../../output/preprocess/Psoriasis/gene_data/GSE158448.csv\"\n", "out_clinical_data_file = \"../../output/preprocess/Psoriasis/clinical_data/GSE158448.csv\"\n", "json_path = \"../../output/preprocess/Psoriasis/cohort_info.json\"\n" ] }, { "cell_type": "markdown", "id": "5efeb8c2", "metadata": {}, "source": [ "### Step 1: Initial Data Loading" ] }, { "cell_type": "code", "execution_count": 2, "id": "090c1717", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:41:33.672444Z", "iopub.status.busy": "2025-03-25T03:41:33.672274Z", "iopub.status.idle": "2025-03-25T03:41:33.904424Z", "shell.execute_reply": "2025-03-25T03:41:33.904015Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Background Information:\n", "!Series_title\t\"Multiple IL-17 family cytokines signaling through IL-17RA drive inflammatory pathways in psoriasis\"\n", "!Series_summary\t\"The IL-23/IL-17 immune axis is of central importance in psoriasis. However, the contribution of IL-17 family cytokines other than IL-17A to drive skin inflammation in psoriasis has not been fully established. To further elucidate the role of individual IL-17 family cytokines in psoriasis, we investigated their expression and localization in psoriasis skin at the mRNA and protein level. Moreover, we investigated the gene expression signatures induced by individual IL-17 family cytokines in human skin ex vivo as well as modulation of responses induced by the combination of IL-17 family cytokines in human keratinocytes by brodalumab, a human monoclonal antibody targeting the IL-17RA, versus the IL-17A blocking antibody ixekizumab. We demonstrate that IL-17A, IL-17AF, IL-17F and IL-17C are expressed at increased levels in psoriasis lesional skin and induce inflammatory gene expression signatures in human skin ex vivo that correlate with those observed in psoriasis. Furthermore, we show that brodalumab, in contrast to ixekizumab, fully blocks gene expression responses induced by the combination of IL-17A, IL-17AF, IL-17F and IL-17C in human keratinocytes. These findings suggest that inhibition of several IL-17 family cytokines, e.g. by targeting of the IL-17RA receptor, could be a favored mechanism to obtain a profound suppression of the inflammatory processes in psoriasis and thereby achieve high levels of skin clearance and sustained efficacy in patients with psoriasis.\"\n", "!Series_overall_design\t\"60 human skin samples separated into 11 groups treated with Il17 variants and 1 untreated control group\"\n", "Sample Characteristics Dictionary:\n", "{0: ['sample_id: 01', 'sample_id: 02', 'sample_id: 03', 'sample_id: 04', 'sample_id: 05', 'sample_id: 06', 'sample_id: 07', 'sample_id: 08', 'sample_id: 09', 'sample_id: 10', 'sample_id: 11', 'sample_id: 12', 'sample_id: 13', 'sample_id: 14', 'sample_id: 15', 'sample_id: 16', 'sample_id: 17', 'sample_id: 18', 'sample_id: 19', 'sample_id: 20', 'sample_id: 21', 'sample_id: 22', 'sample_id: 23', 'sample_id: 24', 'sample_id: 25', 'sample_id: 26', 'sample_id: 27', 'sample_id: 28', 'sample_id: 29', 'sample_id: 30'], 1: ['donor_id: 2', 'donor_id: 3', 'donor_id: 4', 'donor_id: 6', 'donor_id: 7', 'donor_id: 8', 'donor_id: 9', 'donor_id: 11', 'donor_id: 12', 'donor_id: 14', 'donor_id: 16', 'donor_id: 17', 'donor_id: 19', 'donor_id: 20', 'donor_id: 21', 'donor_id: 22', 'donor_id: 23', 'donor_id: 24', 'donor_id: 25', 'donor_id: 28', 'donor_id: 30', 'donor_id: 31', 'donor_id: 32', 'donor_id: 33', 'donor_id: 35', 'donor_id: 37', 'donor_id: 38', 'donor_id: 39', 'donor_id: 41', 'donor_id: 42'], 2: ['rna_integrity: 9.1', 'rna_integrity: 9.4', 'rna_integrity: 9', 'rna_integrity: 9.2', 'rna_integrity: 8.4', 'rna_integrity: 8.9', 'rna_integrity: 9.3', 'rna_integrity: 8.6', 'rna_integrity: 8.8', 'rna_integrity: 9.5', 'rna_integrity: 8', 'rna_integrity: 8.7', 'rna_integrity: 9.6', 'rna_integrity: 9.7', 'rna_integrity: 9.8', 'rna_integrity: 8.3', 'rna_integrity: 7.3'], 3: ['batch: batch_1', 'batch: batch_2', 'batch: batch_3', 'batch: batch_4'], 4: ['treatment: untreated', 'treatment: IL17A_1_ng_ml', 'treatment: IL17A_10_ng_ml', 'treatment: IL17A_100_ng_ml', 'treatment: IL17AF_10_ng_ml', 'treatment: IL17AF_100_ng_ml', 'treatment: IL17F_10_ng_ml', 'treatment: IL17F_100_ng_ml', 'treatment: IL17C_10_ng_ml', 'treatment: IL17C_100_ng_ml', 'treatment: IL17E_10_ng_ml', 'treatment: IL17E_100_ng_ml']}\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": "e62b5d83", "metadata": {}, "source": [ "### Step 2: Dataset Analysis and Clinical Feature Extraction" ] }, { "cell_type": "code", "execution_count": 3, "id": "4d4efd30", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:41:33.906257Z", "iopub.status.busy": "2025-03-25T03:41:33.906107Z", "iopub.status.idle": "2025-03-25T03:41:33.916240Z", "shell.execute_reply": "2025-03-25T03:41:33.915918Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Preview of the selected clinical features:\n", "{0: [0.0], 1: [1.0], 2: [1.0], 3: [1.0], 4: [1.0], 5: [1.0], 6: [1.0], 7: [1.0], 8: [1.0], 9: [1.0], 10: [1.0], 11: [1.0], 12: [nan], 13: [nan], 14: [nan], 15: [nan], 16: [nan], 17: [nan], 18: [nan], 19: [nan], 20: [nan], 21: [nan], 22: [nan], 23: [nan], 24: [nan], 25: [nan], 26: [nan], 27: [nan], 28: [nan], 29: [nan]}\n", "Clinical data saved to ../../output/preprocess/Psoriasis/clinical_data/GSE158448.csv\n" ] } ], "source": [ "# Analyze the data availability and define conversion functions\n", "\n", "# 1. Gene Expression Data Availability\n", "# From the background information, this appears to be a gene expression study related to IL-17 cytokines in psoriasis\n", "# The study design mentions \"60 human skin samples\" which likely contains gene expression data\n", "is_gene_available = True\n", "\n", "# 2. Variable Availability and Data Type Conversion\n", "\n", "# 2.1 Data Availability for trait, age, and gender\n", "# Trait data: We can infer this from the 'treatment' field (row 4)\n", "trait_row = 4 # The treatment field indicates whether samples are from patients with specific treatments\n", "\n", "# Age data: Not available in the sample characteristics\n", "age_row = None\n", "\n", "# Gender data: Not available in the sample characteristics \n", "gender_row = None\n", "\n", "# 2.2 Data Type Conversion Functions\n", "\n", "def convert_trait(value):\n", " \"\"\"\n", " Convert treatment values to binary indicating whether it's untreated (0) or treated (1)\n", " \"\"\"\n", " if not isinstance(value, str):\n", " return None\n", " \n", " # Extract the value after the colon\n", " if ':' in value:\n", " value = value.split(':', 1)[1].strip()\n", " \n", " if 'untreated' in value.lower():\n", " return 0 # Untreated sample\n", " elif 'IL17' in value:\n", " return 1 # Treated with some form of IL17\n", " else:\n", " return None # Unknown\n", "\n", "# Since age and gender data are not available, we don't need conversion functions for them\n", "convert_age = None\n", "convert_gender = None\n", "\n", "# 3. Save Metadata - Initial Filtering\n", "# Check if both gene and trait data are available\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. Clinical Feature Extraction\n", "if trait_row is not None:\n", " # Create a DataFrame from the sample characteristics dictionary provided in the task\n", " # The sample characteristics dictionary was already provided in the task output\n", " sample_characteristics = {\n", " 0: ['sample_id: 01', 'sample_id: 02', 'sample_id: 03', 'sample_id: 04', 'sample_id: 05', 'sample_id: 06', 'sample_id: 07', 'sample_id: 08', 'sample_id: 09', 'sample_id: 10', 'sample_id: 11', 'sample_id: 12', 'sample_id: 13', 'sample_id: 14', 'sample_id: 15', 'sample_id: 16', 'sample_id: 17', 'sample_id: 18', 'sample_id: 19', 'sample_id: 20', 'sample_id: 21', 'sample_id: 22', 'sample_id: 23', 'sample_id: 24', 'sample_id: 25', 'sample_id: 26', 'sample_id: 27', 'sample_id: 28', 'sample_id: 29', 'sample_id: 30'], \n", " 1: ['donor_id: 2', 'donor_id: 3', 'donor_id: 4', 'donor_id: 6', 'donor_id: 7', 'donor_id: 8', 'donor_id: 9', 'donor_id: 11', 'donor_id: 12', 'donor_id: 14', 'donor_id: 16', 'donor_id: 17', 'donor_id: 19', 'donor_id: 20', 'donor_id: 21', 'donor_id: 22', 'donor_id: 23', 'donor_id: 24', 'donor_id: 25', 'donor_id: 28', 'donor_id: 30', 'donor_id: 31', 'donor_id: 32', 'donor_id: 33', 'donor_id: 35', 'donor_id: 37', 'donor_id: 38', 'donor_id: 39', 'donor_id: 41', 'donor_id: 42'], \n", " 2: ['rna_integrity: 9.1', 'rna_integrity: 9.4', 'rna_integrity: 9', 'rna_integrity: 9.2', 'rna_integrity: 8.4', 'rna_integrity: 8.9', 'rna_integrity: 9.3', 'rna_integrity: 8.6', 'rna_integrity: 8.8', 'rna_integrity: 9.5', 'rna_integrity: 8', 'rna_integrity: 8.7', 'rna_integrity: 9.6', 'rna_integrity: 9.7', 'rna_integrity: 9.8', 'rna_integrity: 8.3', 'rna_integrity: 7.3'], \n", " 3: ['batch: batch_1', 'batch: batch_2', 'batch: batch_3', 'batch: batch_4'], \n", " 4: ['treatment: untreated', 'treatment: IL17A_1_ng_ml', 'treatment: IL17A_10_ng_ml', 'treatment: IL17A_100_ng_ml', 'treatment: IL17AF_10_ng_ml', 'treatment: IL17AF_100_ng_ml', 'treatment: IL17F_10_ng_ml', 'treatment: IL17F_100_ng_ml', 'treatment: IL17C_10_ng_ml', 'treatment: IL17C_100_ng_ml', 'treatment: IL17E_10_ng_ml', 'treatment: IL17E_100_ng_ml']\n", " }\n", " \n", " # Convert to DataFrame\n", " clinical_data = pd.DataFrame.from_dict(sample_characteristics, orient='index')\n", " \n", " # Extract clinical features\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,\n", " gender_row=gender_row,\n", " convert_gender=convert_gender\n", " )\n", " \n", " # Preview the data\n", " print(\"Preview of the selected clinical features:\")\n", " print(preview_df(selected_clinical_df))\n", " \n", " # Save 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": "5effcc84", "metadata": {}, "source": [ "### Step 3: Gene Data Extraction" ] }, { "cell_type": "code", "execution_count": 4, "id": "b4b255d4", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:41:33.917736Z", "iopub.status.busy": "2025-03-25T03:41:33.917628Z", "iopub.status.idle": "2025-03-25T03:41:34.298211Z", "shell.execute_reply": "2025-03-25T03:41:34.297822Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "First 20 gene/probe identifiers:\n", "Index(['16650001', '16650003', '16650005', '16650007', '16650009', '16650011',\n", " '16650013', '16650015', '16650017', '16650019', '16650021', '16650023',\n", " '16650025', '16650027', '16650029', '16650031', '16650033', '16650035',\n", " '16650037', '16650041'],\n", " dtype='object', name='ID')\n", "\n", "Gene data dimensions: 53617 genes × 60 samples\n" ] } ], "source": [ "# 1. Re-identify the SOFT and matrix files to ensure we have the correct paths\n", "soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n", "\n", "# 2. Extract the gene expression data from the matrix file\n", "gene_data = get_genetic_data(matrix_file)\n", "\n", "# 3. Print the first 20 row IDs (gene or probe identifiers)\n", "print(\"\\nFirst 20 gene/probe identifiers:\")\n", "print(gene_data.index[:20])\n", "\n", "# 4. Print the dimensions of the gene expression data\n", "print(f\"\\nGene data dimensions: {gene_data.shape[0]} genes × {gene_data.shape[1]} samples\")\n", "\n", "# Note: we keep is_gene_available as True since we successfully extracted gene expression data\n", "is_gene_available = True\n" ] }, { "cell_type": "markdown", "id": "882cc686", "metadata": {}, "source": [ "### Step 4: Gene Identifier Review" ] }, { "cell_type": "code", "execution_count": 5, "id": "2bda3662", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:41:34.299847Z", "iopub.status.busy": "2025-03-25T03:41:34.299725Z", "iopub.status.idle": "2025-03-25T03:41:34.302019Z", "shell.execute_reply": "2025-03-25T03:41:34.301660Z" } }, "outputs": [], "source": [ "# These identifiers appear to be numeric probe IDs, not human gene symbols\n", "# They are likely platform-specific identifiers that need to be mapped to gene symbols\n", "\n", "# Looking at the format (purely numeric IDs starting with \"1665\"), these are \n", "# not standard human gene symbols which typically have alphabetic characters\n", "\n", "# They are most likely probe IDs from a microarray platform that need to be \n", "# converted to standard gene symbols\n", "\n", "requires_gene_mapping = True\n" ] }, { "cell_type": "markdown", "id": "7460c7d5", "metadata": {}, "source": [ "### Step 5: Gene Annotation" ] }, { "cell_type": "code", "execution_count": 6, "id": "0ba4215b", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:41:34.303531Z", "iopub.status.busy": "2025-03-25T03:41:34.303428Z", "iopub.status.idle": "2025-03-25T03:41:44.465339Z", "shell.execute_reply": "2025-03-25T03:41:44.464896Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Preview of SOFT file content:\n", "^DATABASE = GeoMiame\n", "!Database_name = Gene Expression Omnibus (GEO)\n", "!Database_institute = NCBI NLM NIH\n", "!Database_web_link = http://www.ncbi.nlm.nih.gov/geo\n", "!Database_email = geo@ncbi.nlm.nih.gov\n", "^SERIES = GSE158448\n", "!Series_title = Multiple IL-17 family cytokines signaling through IL-17RA drive inflammatory pathways in psoriasis\n", "!Series_geo_accession = GSE158448\n", "!Series_status = Public on Apr 07 2021\n", "!Series_submission_date = Sep 23 2020\n", "!Series_last_update_date = Apr 10 2021\n", "!Series_pubmed_id = 33792895\n", "!Series_summary = The IL-23/IL-17 immune axis is of central importance in psoriasis. However, the contribution of IL-17 family cytokines other than IL-17A to drive skin inflammation in psoriasis has not been fully established. To further elucidate the role of individual IL-17 family cytokines in psoriasis, we investigated their expression and localization in psoriasis skin at the mRNA and protein level. Moreover, we investigated the gene expression signatures induced by individual IL-17 family cytokines in human skin ex vivo as well as modulation of responses induced by the combination of IL-17 family cytokines in human keratinocytes by brodalumab, a human monoclonal antibody targeting the IL-17RA, versus the IL-17A blocking antibody ixekizumab. We demonstrate that IL-17A, IL-17AF, IL-17F and IL-17C are expressed at increased levels in psoriasis lesional skin and induce inflammatory gene expression signatures in human skin ex vivo that correlate with those observed in psoriasis. Furthermore, we show that brodalumab, in contrast to ixekizumab, fully blocks gene expression responses induced by the combination of IL-17A, IL-17AF, IL-17F and IL-17C in human keratinocytes. These findings suggest that inhibition of several IL-17 family cytokines, e.g. by targeting of the IL-17RA receptor, could be a favored mechanism to obtain a profound suppression of the inflammatory processes in psoriasis and thereby achieve high levels of skin clearance and sustained efficacy in patients with psoriasis.\n", "!Series_overall_design = 60 human skin samples separated into 11 groups treated with Il17 variants and 1 untreated control group\n", "!Series_type = Expression profiling by array\n", "!Series_contributor = Maxim,A,Tollenaere\n", "!Series_contributor = Josephine,,Hebsgaard\n", "!Series_contributor = David,A,Ewald\n", "!Series_contributor = Paola,,Lovato\n", "!Series_contributor = Sandra,,Garcet\n", "!Series_contributor = Xuan,,Li\n", "...\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Gene annotation dataframe using default method:\n", "Shape: (3270697, 20)\n", "Columns: ['ID', 'probeset_id', 'seqname', 'strand', 'start', 'stop', 'total_probes', 'gene_assignment', 'mrna_assignment', 'swissprot', 'unigene', 'GO_biological_process', 'GO_cellular_component', 'GO_molecular_function', 'pathway', 'protein_domains', 'crosshyb_type', 'category', 'GB_ACC', 'SPOT_ID']\n", " ID probeset_id seqname strand start stop total_probes \\\n", "0 16657436 16657436 chr1 + 12190 13639 25.0 \n", "1 16657440 16657440 chr1 + 29554 31109 28.0 \n", "2 16657445 16657445 chr1 + 69091 70008 8.0 \n", "\n", " gene_assignment \\\n", "0 NR_046018 // DDX11L1 // DEAD/H (Asp-Glu-Ala-As... \n", "1 ENST00000473358 // MIR1302-11 // microRNA 1302... \n", "2 NM_001005484 // OR4F5 // olfactory receptor, f... \n", "\n", " mrna_assignment \\\n", "0 NR_046018 // RefSeq // Homo sapiens DEAD/H (As... \n", "1 ENST00000473358 // ENSEMBL // cdna:known chrom... \n", "2 NM_001005484 // RefSeq // Homo sapiens olfacto... \n", "\n", " swissprot \\\n", "0 NR_046018 // B7ZGW9 /// NR_046018 // B7ZGX0 //... \n", "1 --- \n", "2 --- \n", "\n", " unigene GO_biological_process \\\n", "0 NR_046018 // Hs.714157 // testis| normal| adul... --- \n", "1 --- --- \n", "2 NM_001005484 // Hs.554500 // --- /// ENST00000... --- \n", "\n", " GO_cellular_component \\\n", "0 --- \n", "1 --- \n", "2 NM_001005484 // GO:0005886 // plasma membrane ... \n", "\n", " GO_molecular_function pathway \\\n", "0 --- --- \n", "1 --- --- \n", "2 NM_001005484 // GO:0004930 // G-protein couple... --- \n", "\n", " protein_domains crosshyb_type category \\\n", "0 --- 3 main \n", "1 --- 3 main \n", "2 ENST00000335137 // Pfam // IPR000276 // GPCR, ... 3 main \n", "\n", " GB_ACC SPOT_ID \n", "0 NR_046018 NaN \n", "1 NaN ENST00000473358 \n", "2 NM_001005484 NaN \n", "\n", "Searching for platform annotation section in SOFT file...\n", "^PLATFORM = GPL17692\n", "!platform_table_begin\n", "ID\tprobeset_id\tseqname\tstrand\tstart\tstop\ttotal_probes\tgene_assignment\tmrna_assignment\tswissprot\tunigene\tGO_biological_process\tGO_cellular_component\tGO_molecular_function\tpathway\tprotein_domains\tcrosshyb_type\tcategory\tGB_ACC\tSPOT_ID\n", "16657436\t16657436\tchr1\t+\t12190\t13639\t25\tNR_046018 // DDX11L1 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 // 1p36.33 // 100287102 /// NR_034090 // DDX11L9 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 // 15q26.3 // 100288486 /// NR_051985 // DDX11L9 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 // 15q26.3 // 100288486 /// NR_045117 // DDX11L10 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 10 // 16p13.3 // 100287029 /// NR_024004 // DDX11L2 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 2 // 2q13 // 84771 /// NR_024005 // DDX11L2 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 2 // 2q13 // 84771 /// NR_051986 // DDX11L5 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 5 // 9p24.3 // 100287596 /// ENST00000456328 // DDX11L1 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 // 1p36.33 // 100287102 /// ENST00000559159 // DDX11L9 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 // 15q26.3 // 100288486 /// ENST00000562189 // DDX11L9 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 // 15q26.3 // 100288486 /// ENST00000513886 // DDX11L10 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 10 // 16p13.3 // 100287029 /// ENST00000515242 // DDX11L1 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 // 1p36.33 // 100287102 /// ENST00000518655 // DDX11L1 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 // 1p36.33 // 100287102 /// ENST00000515173 // DDX11L9 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 // 15q26.3 // 100288486 /// ENST00000545636 // DDX11L10 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 10 // 16p13.3 // 100287029 /// ENST00000450305 // DDX11L1 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 // 1p36.33 // 100287102 /// ENST00000560040 // DDX11L9 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 // 15q26.3 // 100288486 /// ENST00000430178 // DDX11L10 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 10 // 16p13.3 // 100287029 /// ENST00000538648 // DDX11L9 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 // 15q26.3 // 100288486 /// ENST00000535848 // DDX11L2 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 2 // --- // --- /// ENST00000457993 // DDX11L2 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 2 // --- // --- /// ENST00000437401 // DDX11L2 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 2 // --- // --- /// ENST00000426146 // DDX11L5 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 5 // --- // --- /// ENST00000445777 // DDX11L16 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 16 // --- // --- /// ENST00000507418 // DDX11L16 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 16 // --- // --- /// ENST00000507418 // DDX11L16 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 16 // --- // --- /// ENST00000507418 // DDX11L16 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 16 // --- // --- /// ENST00000507418 // DDX11L16 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 16 // --- // --- /// ENST00000421620 // DDX11L5 // DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 5 // --- // ---\tNR_046018 // RefSeq // Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1 (DDX11L1), non-coding RNA. // chr1 // 100 // 100 // 25 // 25 // 0 /// NR_034090 // RefSeq // Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 (DDX11L9), transcript variant 1, non-coding RNA. // chr1 // 96 // 100 // 24 // 25 // 0 /// NR_051985 // RefSeq // Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 9 (DDX11L9), transcript variant 2, non-coding RNA. // chr1 // 96 // 100 // 24 // 25 // 0 /// NR_045117 // RefSeq // Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 10 (DDX11L10), non-coding RNA. // chr1 // 92 // 96 // 22 // 24 // 0 /// NR_024004 // RefSeq // Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 2 (DDX11L2), transcript variant 1, non-coding RNA. // chr1 // 83 // 96 // 20 // 24 // 0 /// NR_024005 // RefSeq // Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 2 (DDX11L2), transcript variant 2, non-coding RNA. // chr1 // 83 // 96 // 20 // 24 // 0 /// NR_051986 // RefSeq // Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 5 (DDX11L5), non-coding RNA. // chr1 // 50 // 96 // 12 // 24 // 0 /// TCONS_l2_00010384-XLOC_l2_005087 // Broad TUCP // linc-SNRNP25-2 chr16:+:61554-64041 // chr1 // 92 // 96 // 22 // 24 // 0 /// TCONS_l2_00010385-XLOC_l2_005087 // Broad TUCP // linc-SNRNP25-2 chr16:+:61554-64090 // chr1 // 92 // 96 // 22 // 24 // 0 /// TCONS_l2_00030644-XLOC_l2_015857 // Broad TUCP // linc-TMLHE chrX:-:155255810-155257756 // chr1 // 50 // 96 // 12 // 24 // 0 /// TCONS_l2_00028588-XLOC_l2_014685 // Broad TUCP // linc-DOCK8-2 chr9:+:11235-13811 // chr1 // 50 // 64 // 8 // 16 // 0 /// TCONS_l2_00030643-XLOC_l2_015857 // Broad TUCP // linc-TMLHE chrX:-:155255810-155257756 // chr1 // 50 // 64 // 8 // 16 // 0 /// ENST00000456328 // ENSEMBL // cdna:known chromosome:GRCh37:1:11869:14409:1 gene:ENSG00000223972 gene_biotype:pseudogene transcript_biotype:processed_transcript // chr1 // 100 // 100 // 25 // 25 // 0 /// ENST00000559159 // ENSEMBL // cdna:known chromosome:GRCh37:15:102516761:102519296:-1 gene:ENSG00000248472 gene_biotype:pseudogene transcript_biotype:processed_transcript // chr1 // 96 // 100 // 24 // 25 // 0 /// ENST00000562189 // ENSEMBL // cdna:known chromosome:GRCh37:15:102516761:102519296:-1 gene:ENSG00000248472 gene_biotype:pseudogene transcript_biotype:processed_transcript // chr1 // 96 // 100 // 24 // 25 // 0 /// ENST00000513886 // ENSEMBL // cdna:known chromosome:GRCh37:16:61555:64090:1 gene:ENSG00000233614 gene_biotype:pseudogene transcript_biotype:processed_transcript // chr1 // 92 // 96 // 22 // 24 // 0 /// AK125998 // GenBank // Homo sapiens cDNA FLJ44010 fis, clone TESTI4024344. // chr1 // 50 // 96 // 12 // 24 // 0 /// BC070227 // GenBank // Homo sapiens similar to DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 isoform 1, mRNA (cDNA clone IMAGE:6103207). // chr1 // 100 // 44 // 11 // 11 // 0 /// ENST00000515242 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:1:11872:14412:1 gene:ENSG00000223972 gene_biotype:pseudogene transcript_biotype:transcribed_unprocessed_pseudogene // chr1 // 100 // 100 // 25 // 25 // 0 /// ENST00000518655 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:1:11874:14409:1 gene:ENSG00000223972 gene_biotype:pseudogene transcript_biotype:transcribed_unprocessed_pseudogene // chr1 // 100 // 100 // 25 // 25 // 0 /// ENST00000515173 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:15:102516758:102519298:-1 gene:ENSG00000248472 gene_biotype:pseudogene transcript_biotype:transcribed_unprocessed_pseudogene // chr1 // 96 // 100 // 24 // 25 // 0 /// ENST00000545636 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:16:61553:64093:1 gene:ENSG00000233614 gene_biotype:pseudogene transcript_biotype:transcribed_unprocessed_pseudogene // chr1 // 92 // 96 // 22 // 24 // 0 /// ENST00000450305 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:1:12010:13670:1 gene:ENSG00000223972 gene_biotype:pseudogene transcript_biotype:transcribed_unprocessed_pseudogene // chr1 // 100 // 68 // 17 // 17 // 0 /// ENST00000560040 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:15:102517497:102518994:-1 gene:ENSG00000248472 gene_biotype:pseudogene transcript_biotype:transcribed_unprocessed_pseudogene // chr1 // 94 // 68 // 16 // 17 // 0 /// ENST00000430178 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:16:61861:63351:1 gene:ENSG00000233614 gene_biotype:pseudogene transcript_biotype:transcribed_unprocessed_pseudogene // chr1 // 88 // 64 // 14 // 16 // 0 /// ENST00000538648 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:15:102517351:102517622:-1 gene:ENSG00000248472 gene_biotype:pseudogene transcript_biotype:pseudogene // chr1 // 100 // 16 // 4 // 4 // 0 /// ENST00000535848 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:2:114356606:114359144:-1 gene:ENSG00000236397 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 83 // 96 // 20 // 24 // 0 /// ENST00000457993 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:2:114356613:114358838:-1 gene:ENSG00000236397 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 85 // 80 // 17 // 20 // 0 /// ENST00000437401 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:2:114356613:114358838:-1 gene:ENSG00000236397 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 80 // 80 // 16 // 20 // 0 /// ENST00000426146 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:9:11987:14522:1 gene:ENSG00000236875 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 50 // 96 // 12 // 24 // 0 /// ENST00000445777 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:X:155255323:155257848:-1 gene:ENSG00000227159 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 50 // 96 // 12 // 24 // 0 /// ENST00000507418 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:X:155255329:155257542:-1 gene:ENSG00000227159 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 50 // 64 // 8 // 16 // 0 /// ENST00000421620 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:9:12134:13439:1 gene:ENSG00000236875 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 100 // 12 // 3 // 3 // 0 /// GENSCAN00000003613 // ENSEMBL // cdna:genscan chromosome:GRCh37:15:102517021:102518980:-1 transcript_biotype:protein_coding // chr1 // 100 // 52 // 13 // 13 // 0 /// GENSCAN00000026650 // ENSEMBL // cdna:genscan chromosome:GRCh37:1:12190:14149:1 transcript_biotype:protein_coding // chr1 // 100 // 52 // 13 // 13 // 0 /// GENSCAN00000029586 // ENSEMBL // cdna:genscan chromosome:GRCh37:16:61871:63830:1 transcript_biotype:protein_coding // chr1 // 100 // 48 // 12 // 12 // 0 /// ENST00000535849 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:12:92239:93430:-1 gene:ENSG00000256263 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 38 // 32 // 3 // 8 // 1 /// ENST00000575871 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:HG858_PATCH:62310:63501:1 gene:ENSG00000262195 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 38 // 32 // 3 // 8 // 1 /// ENST00000572276 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:HSCHR12_1_CTG1:62310:63501:1 gene:ENSG00000263289 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 38 // 32 // 3 // 8 // 1 /// GENSCAN00000048516 // ENSEMBL // cdna:genscan chromosome:GRCh37:HG858_PATCH:62740:64276:1 transcript_biotype:protein_coding // chr1 // 25 // 48 // 3 // 12 // 1 /// GENSCAN00000048612 // ENSEMBL // cdna:genscan chromosome:GRCh37:HSCHR12_1_CTG1:62740:64276:1 transcript_biotype:protein_coding // chr1 // 25 // 48 // 3 // 12 // 1\tNR_046018 // B7ZGW9 /// NR_046018 // B7ZGX0 /// NR_046018 // B7ZGX2 /// NR_046018 // B7ZGX3 /// NR_046018 // B7ZGX5 /// NR_046018 // B7ZGX6 /// NR_046018 // B7ZGX7 /// NR_046018 // B7ZGX8 /// NR_046018 // B7ZGX9 /// NR_046018 // B7ZGY0 /// NR_034090 // B7ZGW9 /// NR_034090 // B7ZGX0 /// NR_034090 // B7ZGX2 /// NR_034090 // B7ZGX3 /// NR_034090 // B7ZGX5 /// NR_034090 // B7ZGX6 /// NR_034090 // B7ZGX7 /// NR_034090 // B7ZGX8 /// NR_034090 // B7ZGX9 /// NR_034090 // B7ZGY0 /// NR_051985 // B7ZGW9 /// NR_051985 // B7ZGX0 /// NR_051985 // B7ZGX2 /// NR_051985 // B7ZGX3 /// NR_051985 // B7ZGX5 /// NR_051985 // B7ZGX6 /// NR_051985 // B7ZGX7 /// NR_051985 // B7ZGX8 /// NR_051985 // B7ZGX9 /// NR_051985 // B7ZGY0 /// NR_045117 // B7ZGW9 /// NR_045117 // B7ZGX0 /// NR_045117 // B7ZGX2 /// NR_045117 // B7ZGX3 /// NR_045117 // B7ZGX5 /// NR_045117 // B7ZGX6 /// NR_045117 // B7ZGX7 /// NR_045117 // B7ZGX8 /// NR_045117 // B7ZGX9 /// NR_045117 // B7ZGY0 /// NR_024005 // B7ZGW9 /// NR_024005 // B7ZGX0 /// NR_024005 // B7ZGX2 /// NR_024005 // B7ZGX3 /// NR_024005 // B7ZGX5 /// NR_024005 // B7ZGX6 /// NR_024005 // B7ZGX7 /// NR_024005 // B7ZGX8 /// NR_024005 // B7ZGX9 /// NR_024005 // B7ZGY0 /// NR_051986 // B7ZGW9 /// NR_051986 // B7ZGX0 /// NR_051986 // B7ZGX2 /// NR_051986 // B7ZGX3 /// NR_051986 // B7ZGX5 /// NR_051986 // B7ZGX6 /// NR_051986 // B7ZGX7 /// NR_051986 // B7ZGX8 /// NR_051986 // B7ZGX9 /// NR_051986 // B7ZGY0 /// AK125998 // Q6ZU42 /// AK125998 // B7ZGW9 /// AK125998 // B7ZGX0 /// AK125998 // B7ZGX2 /// AK125998 // B7ZGX3 /// AK125998 // B7ZGX5 /// AK125998 // B7ZGX6 /// AK125998 // B7ZGX7 /// AK125998 // B7ZGX8 /// AK125998 // B7ZGX9 /// AK125998 // B7ZGY0\tNR_046018 // Hs.714157 // testis| normal| adult /// NR_034090 // Hs.644359 // blood| normal| adult /// NR_051985 // Hs.644359 // blood| normal| adult /// NR_045117 // Hs.592089 // brain| glioma /// NR_024004 // Hs.712940 // bladder| bone marrow| brain| embryonic tissue| intestine| mammary gland| muscle| pharynx| placenta| prostate| skin| spleen| stomach| testis| thymus| breast (mammary gland) tumor| gastrointestinal tumor| glioma| non-neoplasia| normal| prostate cancer| skin tumor| soft tissue/muscle tissue tumor|embryoid body| adult /// NR_024005 // Hs.712940 // bladder| bone marrow| brain| embryonic tissue| intestine| mammary gland| muscle| pharynx| placenta| prostate| skin| spleen| stomach| testis| thymus| breast (mammary gland) tumor| gastrointestinal tumor| glioma| non-neoplasia| normal| prostate cancer| skin tumor| soft tissue/muscle tissue tumor|embryoid body| adult /// NR_051986 // Hs.719844 // brain| normal /// ENST00000456328 // Hs.714157 // testis| normal| adult /// ENST00000559159 // Hs.644359 // blood| normal| adult /// ENST00000562189 // Hs.644359 // blood| normal| adult /// ENST00000513886 // Hs.592089 // brain| glioma /// ENST00000515242 // Hs.714157 // testis| normal| adult /// ENST00000518655 // Hs.714157 // testis| normal| adult /// ENST00000515173 // Hs.644359 // blood| normal| adult /// ENST00000545636 // Hs.592089 // brain| glioma /// ENST00000450305 // Hs.714157 // testis| normal| adult /// ENST00000560040 // Hs.644359 // blood| normal| adult /// ENST00000430178 // Hs.592089 // brain| glioma /// ENST00000538648 // Hs.644359 // blood| normal| adult\t---\t---\t---\t---\t---\t3\tmain\tNR_046018\n", "16657440\t16657440\tchr1\t+\t29554\t31109\t28\tENST00000473358 // MIR1302-11 // microRNA 1302-11 // --- // 100422919 /// ENST00000473358 // MIR1302-10 // microRNA 1302-10 // --- // 100422834 /// ENST00000473358 // MIR1302-9 // microRNA 1302-9 // --- // 100422831 /// ENST00000473358 // MIR1302-2 // microRNA 1302-2 // --- // 100302278\tENST00000473358 // ENSEMBL // cdna:known chromosome:GRCh37:1:29554:31097:1 gene:ENSG00000243485 gene_biotype:antisense transcript_biotype:antisense // chr1 // 100 // 71 // 20 // 20 // 0\t---\t---\t---\t---\t---\t---\t---\t3\tmain\t\tENST00000473358\n", "16657445\t16657445\tchr1\t+\t69091\t70008\t8\tNM_001005484 // OR4F5 // olfactory receptor, family 4, subfamily F, member 5 // 1p36.33 // 79501 /// ENST00000335137 // OR4F5 // olfactory receptor, family 4, subfamily F, member 5 // 1p36.33 // 79501\tNM_001005484 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 5 (OR4F5), mRNA. // chr1 // 100 // 100 // 8 // 8 // 0 /// ENST00000335137 // ENSEMBL // cdna:known chromosome:GRCh37:1:69091:70008:1 gene:ENSG00000186092 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 8 // 8 // 0\t---\tNM_001005484 // Hs.554500 // --- /// ENST00000335137 // Hs.554500 // ---\t---\tNM_001005484 // GO:0005886 // plasma membrane // traceable author statement /// NM_001005484 // GO:0016021 // integral to membrane // inferred from electronic annotation /// ENST00000335137 // GO:0005886 // plasma membrane // traceable author statement /// ENST00000335137 // GO:0016021 // integral to membrane // inferred from electronic annotation\tNM_001005484 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// NM_001005484 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation /// ENST00000335137 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// ENST00000335137 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation\t---\tENST00000335137 // Pfam // IPR000276 // GPCR, rhodopsin-like, 7TM /// ENST00000335137 // Pfam // IPR019424 // 7TM GPCR, olfactory receptor/chemoreceptor Srsx\t3\tmain\tNM_001005484\n", "16657447\t16657447\tchr1\t+\t160446\t161525\t13\t---\tTCONS_00000119-XLOC_000001 // Rinn lincRNA // linc-OR4F16-10 chr1:+:160445-161525 // chr1 // 100 // 100 // 13 // 13 // 0\t---\t---\t---\t---\t---\t---\t---\t3\tmain\t\tTCONS_00000119-XLOC_000001\n", "16657450\t16657450\tchr1\t+\t317811\t328581\t36\tAK302511 // LOC100132062 // uncharacterized LOC100132062 // 5q35.3 // 100132062 /// AK294489 // LOC729737 // uncharacterized LOC729737 // 1p36.33 // 729737 /// AK303380 // LOC100132062 // uncharacterized LOC100132062 // 5q35.3 // 100132062 /// AK316554 // LOC100132062 // uncharacterized LOC100132062 // 5q35.3 // 100132062 /// AK316556 // LOC100132062 // uncharacterized LOC100132062 // 5q35.3 // 100132062 /// AK302573 // LOC729737 // uncharacterized LOC729737 // 1p36.33 // 729737 /// AK123446 // LOC441124 // uncharacterized LOC441124 // 1q42.11 // 441124 /// ENST00000425496 // LOC100506479 // uncharacterized LOC100506479 // --- // 100506479 /// ENST00000425496 // LOC100289306 // uncharacterized LOC100289306 // 7p11.2 // 100289306 /// ENST00000425496 // LOC100287894 // uncharacterized LOC100287894 // 7q11.21 // 100287894 /// ENST00000425496 // FLJ45445 // uncharacterized LOC399844 // 19p13.3 // 399844 /// ENST00000456623 // LOC100506479 // uncharacterized LOC100506479 // --- // 100506479 /// ENST00000456623 // LOC100289306 // uncharacterized LOC100289306 // 7p11.2 // 100289306 /// ENST00000456623 // LOC100287894 // uncharacterized LOC100287894 // 7q11.21 // 100287894 /// ENST00000456623 // FLJ45445 // uncharacterized LOC399844 // 19p13.3 // 399844 /// ENST00000418377 // LOC100506479 // uncharacterized LOC100506479 // --- // 100506479 /// ENST00000418377 // LOC100288102 // uncharacterized LOC100288102 // 1q42.11 // 100288102 /// ENST00000418377 // LOC731275 // uncharacterized LOC731275 // 1q43 // 731275 /// ENST00000534867 // LOC100506479 // uncharacterized LOC100506479 // --- // 100506479 /// ENST00000534867 // LOC100289306 // uncharacterized LOC100289306 // 7p11.2 // 100289306 /// ENST00000534867 // LOC100287894 // uncharacterized LOC100287894 // 7q11.21 // 100287894 /// ENST00000534867 // FLJ45445 // uncharacterized LOC399844 // 19p13.3 // 399844 /// ENST00000544678 // LOC100653346 // uncharacterized LOC100653346 // --- // 100653346 /// ENST00000544678 // LOC100653241 // uncharacterized LOC100653241 // --- // 100653241 /// ENST00000544678 // LOC100652945 // uncharacterized LOC100652945 // --- // 100652945 /// ENST00000544678 // LOC100508632 // uncharacterized LOC100508632 // --- // 100508632 /// ENST00000544678 // LOC100132050 // uncharacterized LOC100132050 // 7p11.2 // 100132050 /// ENST00000544678 // LOC100128326 // putative uncharacterized protein FLJ44672-like // 7p11.2 // 100128326 /// ENST00000419160 // LOC100506479 // uncharacterized LOC100506479 // --- // 100506479 /// ENST00000419160 // LOC100289306 // uncharacterized LOC100289306 // 7p11.2 // 100289306 /// ENST00000419160 // LOC100287894 // uncharacterized LOC100287894 // 7q11.21 // 100287894 /// ENST00000419160 // FLJ45445 // uncharacterized LOC399844 // 19p13.3 // 399844 /// ENST00000432964 // LOC100506479 // uncharacterized LOC100506479 // --- // 100506479 /// ENST00000432964 // LOC100289306 // uncharacterized LOC100289306 // 7p11.2 // 100289306 /// ENST00000432964 // LOC100287894 // uncharacterized LOC100287894 // 7q11.21 // 100287894 /// ENST00000432964 // FLJ45445 // uncharacterized LOC399844 // 19p13.3 // 399844 /// ENST00000423728 // LOC100506479 // uncharacterized LOC100506479 // --- // 100506479 /// ENST00000423728 // LOC100289306 // uncharacterized LOC100289306 // 7p11.2 // 100289306 /// ENST00000423728 // LOC100287894 // uncharacterized LOC100287894 // 7q11.21 // 100287894 /// ENST00000423728 // FLJ45445 // uncharacterized LOC399844 // 19p13.3 // 399844 /// ENST00000457364 // LOC100653346 // uncharacterized LOC100653346 // --- // 100653346 /// ENST00000457364 // LOC100653241 // uncharacterized LOC100653241 // --- // 100653241 /// ENST00000457364 // LOC100652945 // uncharacterized LOC100652945 // --- // 100652945 /// ENST00000457364 // LOC100508632 // uncharacterized LOC100508632 // --- // 100508632 /// ENST00000457364 // LOC100132050 // uncharacterized LOC100132050 // 7p11.2 // 100132050 /// ENST00000457364 // LOC100128326 // putative uncharacterized protein FLJ44672-like // 7p11.2 // 100128326 /// ENST00000438516 // LOC100653346 // uncharacterized LOC100653346 // --- // 100653346 /// ENST00000438516 // LOC100653241 // uncharacterized LOC100653241 // --- // 100653241 /// ENST00000438516 // LOC100652945 // uncharacterized LOC100652945 // --- // 100652945 /// ENST00000438516 // LOC100508632 // uncharacterized LOC100508632 // --- // 100508632 /// ENST00000438516 // LOC100132050 // uncharacterized LOC100132050 // 7p11.2 // 100132050 /// ENST00000438516 // LOC100128326 // putative uncharacterized protein FLJ44672-like // 7p11.2 // 100128326\tAK302511 // GenBank // Homo sapiens cDNA FLJ61476 complete cds. // chr1 // 92 // 33 // 11 // 12 // 0 /// AK294489 // GenBank // Homo sapiens cDNA FLJ52615 complete cds. // chr1 // 77 // 36 // 10 // 13 // 0 /// AK303380 // GenBank // Homo sapiens cDNA FLJ53527 complete cds. // chr1 // 100 // 14 // 5 // 5 // 0 /// AK316554 // GenBank // Homo sapiens cDNA, FLJ79453 complete cds. // chr1 // 100 // 11 // 4 // 4 // 0 /// AK316556 // GenBank // Homo sapiens cDNA, FLJ79455 complete cds. // chr1 // 100 // 11 // 4 // 4 // 0 /// AK302573 // GenBank // Homo sapiens cDNA FLJ52612 complete cds. // chr1 // 80 // 14 // 4 // 5 // 0 /// TCONS_l2_00002815-XLOC_l2_001399 // Broad TUCP // linc-PLD5-5 chr1:-:243219130-243221165 // chr1 // 92 // 33 // 11 // 12 // 0 /// TCONS_l2_00001802-XLOC_l2_001332 // Broad TUCP // linc-TP53BP2-3 chr1:-:224139117-224140327 // chr1 // 100 // 14 // 5 // 5 // 0 /// TCONS_l2_00001804-XLOC_l2_001332 // Broad TUCP // linc-TP53BP2-3 chr1:-:224139117-224142371 // chr1 // 100 // 14 // 5 // 5 // 0 /// TCONS_00000120-XLOC_000002 // Rinn lincRNA // linc-OR4F16-9 chr1:+:320161-321056 // chr1 // 100 // 11 // 4 // 4 // 0 /// TCONS_l2_00002817-XLOC_l2_001399 // Broad TUCP // linc-PLD5-5 chr1:-:243220177-243221150 // chr1 // 100 // 6 // 2 // 2 // 0 /// TCONS_00000437-XLOC_000658 // Rinn lincRNA // linc-ZNF692-6 chr1:-:139789-140339 // chr1 // 100 // 6 // 2 // 2 // 0 /// AK299469 // GenBank // Homo sapiens cDNA FLJ52610 complete cds. // chr1 // 100 // 33 // 12 // 12 // 0 /// AK302889 // GenBank // Homo sapiens cDNA FLJ54896 complete cds. // chr1 // 100 // 22 // 8 // 8 // 0 /// AK123446 // GenBank // Homo sapiens cDNA FLJ41452 fis, clone BRSTN2010363. // chr1 // 100 // 19 // 7 // 7 // 0 /// ENST00000425496 // ENSEMBL // cdna:known chromosome:GRCh37:1:324756:328453:1 gene:ENSG00000237094 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 33 // 13 // 12 // 0 /// ENST00000456623 // ENSEMBL // cdna:known chromosome:GRCh37:1:324515:326852:1 gene:ENSG00000237094 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 33 // 12 // 12 // 0 /// ENST00000418377 // ENSEMBL // cdna:known chromosome:GRCh37:1:243219131:243221165:-1 gene:ENSG00000214837 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 92 // 33 // 11 // 12 // 0 /// ENST00000534867 // ENSEMBL // cdna:known chromosome:GRCh37:1:324438:325896:1 gene:ENSG00000237094 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 28 // 10 // 10 // 0 /// ENST00000544678 // ENSEMBL // cdna:known chromosome:GRCh37:5:180751053:180752511:1 gene:ENSG00000238035 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 22 // 8 // 8 // 0 /// ENST00000419160 // ENSEMBL // cdna:known chromosome:GRCh37:1:322732:324955:1 gene:ENSG00000237094 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 17 // 6 // 6 // 0 /// ENST00000432964 // ENSEMBL // cdna:known chromosome:GRCh37:1:320162:321056:1 gene:ENSG00000237094 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 11 // 4 // 4 // 0 /// ENST00000423728 // ENSEMBL // cdna:known chromosome:GRCh37:1:320162:324461:1 gene:ENSG00000237094 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 11 // 4 // 4 // 0 /// BC092421 // GenBank // Homo sapiens cDNA clone IMAGE:30378758. // chr1 // 100 // 33 // 12 // 12 // 0 /// ENST00000426316 // ENSEMBL // cdna:known chromosome:GRCh37:1:317811:328455:1 gene:ENSG00000240876 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 8 // 3 // 3 // 0 /// ENST00000465971 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:7:128291239:128292388:1 gene:ENSG00000243302 gene_biotype:pseudogene transcript_biotype:processed_pseudogene // chr1 // 100 // 31 // 11 // 11 // 0 /// ENST00000535314 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:7:128291243:128292355:1 gene:ENSG00000243302 gene_biotype:pseudogene transcript_biotype:processed_pseudogene // chr1 // 100 // 31 // 11 // 11 // 0 /// ENST00000423372 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:1:134901:139379:-1 gene:ENSG00000237683 gene_biotype:pseudogene transcript_biotype:processed_pseudogene // chr1 // 90 // 28 // 9 // 10 // 0 /// ENST00000435839 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:1:137283:139620:-1 gene:ENSG00000237683 gene_biotype:pseudogene transcript_biotype:processed_pseudogene // chr1 // 90 // 28 // 9 // 10 // 0 /// ENST00000537461 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:1:138239:139697:-1 gene:ENSG00000237683 gene_biotype:pseudogene transcript_biotype:processed_pseudogene // chr1 // 100 // 19 // 7 // 7 // 0 /// ENST00000494149 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:1:135247:138039:-1 gene:ENSG00000237683 gene_biotype:pseudogene transcript_biotype:processed_pseudogene // chr1 // 100 // 8 // 3 // 3 // 0 /// ENST00000514436 // ENSEMBL // cdna:pseudogene chromosome:GRCh37:1:326096:328112:1 gene:ENSG00000250575 gene_biotype:pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 100 // 8 // 3 // 3 // 0 /// ENST00000457364 // ENSEMBL // cdna:known chromosome:GRCh37:5:180751371:180755068:1 gene:ENSG00000238035 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 28 // 11 // 10 // 0 /// ENST00000438516 // ENSEMBL // cdna:known chromosome:GRCh37:5:180751130:180753467:1 gene:ENSG00000238035 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 28 // 10 // 10 // 0 /// ENST00000526704 // ENSEMBL // ensembl_havana_lincrna:lincRNA chromosome:GRCh37:11:129531:139099:-1 gene:ENSG00000230724 gene_biotype:lincRNA transcript_biotype:processed_transcript // chr1 // 93 // 42 // 14 // 15 // 0 /// ENST00000540375 // ENSEMBL // ensembl_havana_lincrna:lincRNA chromosome:GRCh37:11:127115:131056:-1 gene:ENSG00000230724 gene_biotype:lincRNA transcript_biotype:processed_transcript // chr1 // 100 // 28 // 11 // 10 // 0 /// ENST00000457006 // ENSEMBL // ensembl_havana_lincrna:lincRNA chromosome:GRCh37:11:128960:131297:-1 gene:ENSG00000230724 gene_biotype:lincRNA transcript_biotype:processed_transcript // chr1 // 90 // 28 // 9 // 10 // 0 /// ENST00000427071 // ENSEMBL // ensembl_havana_lincrna:lincRNA chromosome:GRCh37:11:130207:131297:-1 gene:ENSG00000230724 gene_biotype:lincRNA transcript_biotype:processed_transcript // chr1 // 100 // 25 // 9 // 9 // 0 /// ENST00000542435 // ENSEMBL // ensembl_havana_lincrna:lincRNA chromosome:GRCh37:11:129916:131374:-1 gene:ENSG00000230724 gene_biotype:lincRNA transcript_biotype:processed_transcript // chr1 // 100 // 22 // 8 // 8 // 0\tAK302511 // B4DYM5 /// AK294489 // B4DGA0 /// AK294489 // Q6ZSN7 /// AK303380 // B4E0H4 /// AK303380 // Q6ZQS4 /// AK303380 // A8E4K2 /// AK316554 // B4E3X0 /// AK316554 // Q6ZSN7 /// AK316556 // B4E3X2 /// AK316556 // Q6ZSN7 /// AK302573 // B7Z7W4 /// AK302573 // Q6ZQS4 /// AK302573 // A8E4K2 /// AK299469 // B7Z5V7 /// AK299469 // Q6ZSN7 /// AK302889 // B7Z846 /// AK302889 // Q6ZSN7 /// AK123446 // B3KVU4\tAK302511 // Hs.732199 // ascites| blood| brain| connective tissue| embryonic tissue| eye| intestine| kidney| larynx| lung| ovary| placenta| prostate| stomach| testis| thymus| uterus| chondrosarcoma| colorectal tumor| gastrointestinal tumor| head and neck tumor| leukemia| lung tumor| normal| ovarian tumor| fetus| adult /// AK294489 // Hs.534942 // blood| brain| embryonic tissue| intestine| lung| mammary gland| mouth| ovary| pancreas| pharynx| placenta| spleen| stomach| testis| thymus| trachea| breast (mammary gland) tumor| colorectal tumor| head and neck tumor| leukemia| lung tumor| normal| ovarian tumor|embryoid body| blastocyst| fetus| adult /// AK294489 // Hs.734488 // blood| brain| esophagus| intestine| kidney| lung| mammary gland| mouth| placenta| prostate| testis| thymus| thyroid| uterus| breast (mammary gland) tumor| colorectal tumor| esophageal tumor| head and neck tumor| kidney tumor| leukemia| lung tumor| normal| adult /// AK303380 // Hs.732199 // ascites| blood| brain| connective tissue| embryonic tissue| eye| intestine| kidney| larynx| lung| ovary| placenta| prostate| stomach| testis| thymus| uterus| chondrosarcoma| colorectal tumor| gastrointestinal tumor| head and neck tumor| leukemia| lung tumor| normal| ovarian tumor| fetus| adult /// AK316554 // Hs.732199 // ascites| blood| brain| connective tissue| embryonic tissue| eye| intestine| kidney| larynx| lung| ovary| placenta| prostate| stomach| testis| thymus| uterus| chondrosarcoma| colorectal tumor| gastrointestinal tumor| head and neck tumor| leukemia| lung tumor| normal| ovarian tumor| fetus| adult /// AK316556 // Hs.732199 // ascites| blood| brain| connective tissue| embryonic tissue| eye| intestine| kidney| larynx| lung| ovary| placenta| prostate| stomach| testis| thymus| uterus| chondrosarcoma| colorectal tumor| gastrointestinal tumor| head and neck tumor| leukemia| lung tumor| normal| ovarian tumor| fetus| adult /// AK302573 // Hs.534942 // blood| brain| embryonic tissue| intestine| lung| mammary gland| mouth| ovary| pancreas| pharynx| placenta| spleen| stomach| testis| thymus| trachea| breast (mammary gland) tumor| colorectal tumor| head and neck tumor| leukemia| lung tumor| normal| ovarian tumor|embryoid body| blastocyst| fetus| adult /// AK302573 // Hs.734488 // blood| brain| esophagus| intestine| kidney| lung| mammary gland| mouth| placenta| prostate| testis| thymus| thyroid| uterus| breast (mammary gland) tumor| colorectal tumor| esophageal tumor| head and neck tumor| kidney tumor| leukemia| lung tumor| normal| adult /// AK123446 // Hs.520589 // bladder| blood| bone| brain| embryonic tissue| intestine| kidney| liver| lung| lymph node| ovary| pancreas| parathyroid| placenta| testis| thyroid| uterus| colorectal tumor| glioma| head and neck tumor| kidney tumor| leukemia| liver tumor| normal| ovarian tumor| uterine tumor|embryoid body| fetus| adult /// ENST00000425496 // Hs.356758 // blood| bone| brain| cervix| connective tissue| embryonic tissue| intestine| kidney| lung| mammary gland| mouth| pancreas| pharynx| placenta| prostate| spleen| stomach| testis| trachea| uterus| vascular| breast (mammary gland) tumor| chondrosarcoma| colorectal tumor| gastrointestinal tumor| glioma| head and neck tumor| leukemia| lung tumor| normal| uterine tumor| adult /// ENST00000425496 // Hs.733048 // ascites| bladder| blood| brain| embryonic tissue| eye| intestine| kidney| larynx| liver| lung| mammary gland| mouth| pancreas| placenta| prostate| skin| stomach| testis| thymus| thyroid| trachea| uterus| bladder carcinoma| breast (mammary gland) tumor| colorectal tumor| gastrointestinal tumor| head and neck tumor| kidney tumor| leukemia| liver tumor| lung tumor| normal| pancreatic tumor| prostate cancer| retinoblastoma| skin tumor| soft tissue/muscle tissue tumor| uterine tumor|embryoid body| blastocyst| fetus| adult /// ENST00000456623 // Hs.356758 // blood| bone| brain| cervix| connective tissue| embryonic tissue| intestine| kidney| lung| mammary gland| mouth| pancreas| pharynx| placenta| prostate| spleen| stomach| testis| trachea| uterus| vascular| breast (mammary gland) tumor| chondrosarcoma| colorectal tumor| gastrointestinal tumor| glioma| head and neck tumor| leukemia| lung tumor| normal| uterine tumor| adult /// ENST00000456623 // Hs.733048 // ascites| bladder| blood| brain| embryonic tissue| eye| intestine| kidney| larynx| liver| lung| mammary gland| mouth| pancreas| placenta| prostate| skin| stomach| testis| thymus| thyroid| trachea| uterus| bladder carcinoma| breast (mammary gland) tumor| colorectal tumor| gastrointestinal tumor| head and neck tumor| kidney tumor| leukemia| liver tumor| lung tumor| normal| pancreatic tumor| prostate cancer| retinoblastoma| skin tumor| soft tissue/muscle tissue tumor| uterine tumor|embryoid body| blastocyst| fetus| adult /// ENST00000534867 // Hs.356758 // blood| bone| brain| cervix| connective tissue| embryonic tissue| intestine| kidney| lung| mammary gland| mouth| pancreas| pharynx| placenta| prostate| spleen| stomach| testis| trachea| uterus| vascular| breast (mammary gland) tumor| chondrosarcoma| colorectal tumor| gastrointestinal tumor| glioma| head and neck tumor| leukemia| lung tumor| normal| uterine tumor| adult /// ENST00000534867 // Hs.733048 // ascites| bladder| blood| brain| embryonic tissue| eye| intestine| kidney| larynx| liver| lung| mammary gland| mouth| pancreas| placenta| prostate| skin| stomach| testis| thymus| thyroid| trachea| uterus| bladder carcinoma| breast (mammary gland) tumor| colorectal tumor| gastrointestinal tumor| head and neck tumor| kidney tumor| leukemia| liver tumor| lung tumor| normal| pancreatic tumor| prostate cancer| retinoblastoma| skin tumor| soft tissue/muscle tissue tumor| uterine tumor|embryoid body| blastocyst| fetus| adult /// ENST00000419160 // Hs.356758 // blood| bone| brain| cervix| connective tissue| embryonic tissue| intestine| kidney| lung| mammary gland| mouth| pancreas| pharynx| placenta| prostate| spleen| stomach| testis| trachea| uterus| vascular| breast (mammary gland) tumor| chondrosarcoma| colorectal tumor| gastrointestinal tumor| glioma| head and neck tumor| leukemia| lung tumor| normal| uterine tumor| adult /// ENST00000419160 // Hs.733048 // ascites| bladder| blood| brain| embryonic tissue| eye| intestine| kidney| larynx| liver| lung| mammary gland| mouth| pancreas| placenta| prostate| skin| stomach| testis| thymus| thyroid| trachea| uterus| bladder carcinoma| breast (mammary gland) tumor| colorectal tumor| gastrointestinal tumor| head and neck tumor| kidney tumor| leukemia| liver tumor| lung tumor| normal| pancreatic tumor| prostate cancer| retinoblastoma| skin tumor| soft tissue/muscle tissue tumor| uterine tumor|embryoid body| blastocyst| fetus| adult /// ENST00000432964 // Hs.356758 // blood| bone| brain| cervix| connective tissue| embryonic tissue| intestine| kidney| lung| mammary gland| mouth| pancreas| pharynx| placenta| prostate| spleen| stomach| testis| trachea| uterus| vascular| breast (mammary gland) tumor| chondrosarcoma| colorectal tumor| gastrointestinal tumor| glioma| head and neck tumor| leukemia| lung tumor| normal| uterine tumor| adult /// ENST00000432964 // Hs.733048 // ascites| bladder| blood| brain| embryonic tissue| eye| intestine| kidney| larynx| liver| lung| mammary gland| mouth| pancreas| placenta| prostate| skin| stomach| testis| thymus| thyroid| trachea| uterus| bladder carcinoma| breast (mammary gland) tumor| colorectal tumor| gastrointestinal tumor| head and neck tumor| kidney tumor| leukemia| liver tumor| lung tumor| normal| pancreatic tumor| prostate cancer| retinoblastoma| skin tumor| soft tissue/muscle tissue tumor| uterine tumor|embryoid body| blastocyst| fetus| adult /// ENST00000423728 // Hs.356758 // blood| bone| brain| cervix| connective tissue| embryonic tissue| intestine| kidney| lung| mammary gland| mouth| pancreas| pharynx| placenta| prostate| spleen| stomach| testis| trachea| uterus| vascular| breast (mammary gland) tumor| chondrosarcoma| colorectal tumor| gastrointestinal tumor| glioma| head and neck tumor| leukemia| lung tumor| normal| uterine tumor| adult /// ENST00000423728 // Hs.733048 // ascites| bladder| blood| brain| embryonic tissue| eye| intestine| kidney| larynx| liver| lung| mammary gland| mouth| pancreas| placenta| prostate| skin| stomach| testis| thymus| thyroid| trachea| uterus| bladder carcinoma| breast (mammary gland) tumor| colorectal tumor| gastrointestinal tumor| head and neck tumor| kidney tumor| leukemia| liver tumor| lung tumor| normal| pancreatic tumor| prostate cancer| retinoblastoma| skin tumor| soft tissue/muscle tissue tumor| uterine tumor|embryoid body| blastocyst| fetus| adult\t---\t---\t---\t---\t---\t3\tmain\tAK302511\n", "16657469\t16657469\tchr1\t+\t329790\t342507\t27\tBC118988 // LINC00266-1 // long intergenic non-protein coding RNA 266-1 // 20q13.33 // 140849 /// ENST00000279067 // LINC00266-1 // long intergenic non-protein coding RNA 266-1 // 20q13.33 // 140849 /// ENST00000425473 // LINC00266-1 // long intergenic non-protein coding RNA 266-1 // 20q13.33 // 140849 /// ENST00000424587 // LOC100508047 // uncharacterized LOC100508047 // --- // 100508047\tBC118988 // GenBank // Homo sapiens chromosome 20 open reading frame 69, mRNA (cDNA clone MGC:141807 IMAGE:40035995), complete cds. // chr1 // 54 // 89 // 13 // 24 // 0 /// TCONS_l2_00002388-XLOC_l2_000726 // Broad TUCP // linc-OR4F29-1 chr1:-:646721-655580 // chr1 // 100 // 67 // 18 // 18 // 0 /// TCONS_l2_00001926-XLOC_l2_000004 // Broad TUCP // linc-OR4F16-1 chr1:+:329783-334271 // chr1 // 100 // 59 // 16 // 16 // 0 /// TCONS_l2_00001927-XLOC_l2_000004 // Broad TUCP // linc-OR4F16-1 chr1:+:334139-342806 // chr1 // 100 // 59 // 16 // 16 // 0 /// TCONS_l2_00002389-XLOC_l2_000726 // Broad TUCP // linc-OR4F29-1 chr1:-:655437-659930 // chr1 // 100 // 59 // 16 // 16 // 0 /// TCONS_l2_00003949-XLOC_l2_001561 // Broad TUCP // linc-BMS1-9 chr10:+:38742108-38755311 // chr1 // 56 // 100 // 15 // 27 // 0 /// TCONS_l2_00025304-XLOC_l2_012836 // Broad TUCP // linc-PDCD2-1 chr6:-:131909-144885 // chr1 // 52 // 100 // 14 // 27 // 0 /// TCONS_l2_00002372-XLOC_l2_000720 // Broad TUCP // linc-ZNF692-5 chr1:-:129080-133566 // chr1 // 88 // 59 // 14 // 16 // 0 /// TCONS_l2_00016828-XLOC_l2_008724 // Broad TUCP // linc-HNF1B-4 chr20:+:62921737-62934707 // chr1 // 54 // 89 // 13 // 24 // 0 /// TCONS_l2_00002380-XLOC_l2_000720 // Broad TUCP // linc-ZNF692-5 chr1:-:235855-267253 // chr1 // 100 // 33 // 9 // 9 // 0 /// TCONS_l2_00003950-XLOC_l2_001561 // Broad TUCP // linc-BMS1-9 chr10:+:38742265-38764837 // chr1 // 56 // 67 // 10 // 18 // 0 /// TCONS_l2_00002386-XLOC_l2_000726 // Broad TUCP // linc-OR4F29-1 chr1:-:637315-655530 // chr1 // 100 // 22 // 6 // 6 // 0 /// TCONS_l2_00002814-XLOC_l2_001398 // Broad TUCP // linc-PLD5-4 chr1:-:243211038-243215554 // chr1 // 56 // 59 // 9 // 16 // 0 /// TCONS_l2_00002811-XLOC_l2_001398 // Broad TUCP // linc-PLD5-4 chr1:-:243192813-243211127 // chr1 // 100 // 15 // 4 // 4 // 0 /// TCONS_l2_00016829-XLOC_l2_008724 // Broad TUCP // linc-HNF1B-4 chr20:+:62926293-62944485 // chr1 // 67 // 22 // 4 // 6 // 0 /// TCONS_l2_00002371-XLOC_l2_000720 // Broad TUCP // linc-ZNF692-5 chr1:-:110952-129173 // chr1 // 67 // 22 // 4 // 6 // 0 /// ENST00000279067 // ENSEMBL // cdna:known chromosome:GRCh37:20:62921738:62934912:1 gene:ENSG00000149656 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 54 // 89 // 13 // 24 // 0 /// ENST00000425473 // ENSEMBL // cdna:known chromosome:GRCh37:20:62926294:62944485:1 gene:ENSG00000149656 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 67 // 22 // 4 // 6 // 0 /// ENST00000424587 // ENSEMBL // cdna:known chromosome:GRCh37:1:235856:267253:-1 gene:ENSG00000228463 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 33 // 9 // 9 // 0 /// ENST00000455464 // ENSEMBL // cdna:known chromosome:GRCh37:1:334140:342806:1 gene:ENSG00000224813 gene_biotype:pseudogene transcript_biotype:processed_transcript // chr1 // 100 // 59 // 16 // 16 // 0 /// ENST00000441245 // ENSEMBL // cdna:known chromosome:GRCh37:1:637316:655530:-1 gene:ENSG00000230021 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 100 // 22 // 6 // 6 // 0 /// ENST00000471248 // ENSEMBL // cdna:known chromosome:GRCh37:1:110953:129173:-1 gene:ENSG00000238009 gene_biotype:antisense transcript_biotype:antisense // chr1 // 67 // 22 // 4 // 6 // 0\t---\t---\t---\t---\t---\t---\t---\t3\tmain\tBC118988\n", "16657473\t16657473\tchr1\t+\t367640\t368634\t25\tENST00000426406 // OR4F29 // olfactory receptor, family 4, subfamily F, member 29 // 1p36.33 // 729759 /// ENST00000426406 // OR4F16 // olfactory receptor, family 4, subfamily F, member 16 // 1p36.33 // 81399 /// ENST00000426406 // OR4F3 // olfactory receptor, family 4, subfamily F, member 3 // 5q35.3 // 26683 /// ENST00000332831 // OR4F29 // olfactory receptor, family 4, subfamily F, member 29 // 1p36.33 // 729759 /// ENST00000332831 // OR4F16 // olfactory receptor, family 4, subfamily F, member 16 // 1p36.33 // 81399 /// ENST00000332831 // OR4F3 // olfactory receptor, family 4, subfamily F, member 3 // 5q35.3 // 26683 /// ENST00000456475 // OR4F29 // olfactory receptor, family 4, subfamily F, member 29 // 1p36.33 // 729759 /// ENST00000456475 // OR4F16 // olfactory receptor, family 4, subfamily F, member 16 // 1p36.33 // 81399 /// ENST00000456475 // OR4F3 // olfactory receptor, family 4, subfamily F, member 3 // 5q35.3 // 26683 /// NM_001005277 // OR4F16 // olfactory receptor, family 4, subfamily F, member 16 // 1p36.33 // 81399 /// NM_001005221 // OR4F29 // olfactory receptor, family 4, subfamily F, member 29 // 1p36.33 // 729759 /// NM_001005224 // OR4F3 // olfactory receptor, family 4, subfamily F, member 3 // 5q35.3 // 26683 /// NM_001005504 // OR4F21 // olfactory receptor, family 4, subfamily F, member 21 // 8p23.3 // 441308 /// ENST00000320901 // OR4F21 // olfactory receptor, family 4, subfamily F, member 21 // 8p23.3 // 441308 /// BC137547 // OR4F3 // olfactory receptor, family 4, subfamily F, member 3 // 5q35.3 // 26683 /// BC137547 // OR4F16 // olfactory receptor, family 4, subfamily F, member 16 // 1p36.33 // 81399 /// BC137547 // OR4F29 // olfactory receptor, family 4, subfamily F, member 29 // 1p36.33 // 729759\tENST00000426406 // ENSEMBL // cdna:known chromosome:GRCh37:1:367640:368634:1 gene:ENSG00000235249 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 25 // 25 // 0 /// ENST00000332831 // ENSEMBL // cdna:known chromosome:GRCh37:1:621059:622053:-1 gene:ENSG00000185097 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 25 // 25 // 0 /// ENST00000456475 // ENSEMBL // cdna:known chromosome:GRCh37:5:180794269:180795263:1 gene:ENSG00000230178 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 25 // 25 // 0 /// NM_001005277 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 16 (OR4F16), mRNA. // chr1 // 100 // 68 // 17 // 17 // 0 /// NM_001005221 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 29 (OR4F29), mRNA. // chr1 // 100 // 68 // 17 // 17 // 0 /// NM_001005224 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 3 (OR4F3), mRNA. // chr1 // 100 // 68 // 17 // 17 // 0 /// NM_001005504 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 21 (OR4F21), mRNA. // chr1 // 94 // 68 // 16 // 17 // 0 /// ENST00000320901 // ENSEMBL // cdna:known chromosome:GRCh37:8:116049:117043:-1 gene:ENSG00000176269 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 94 // 68 // 16 // 17 // 0 /// BC137547 // GenBank // Homo sapiens olfactory receptor, family 4, subfamily F, member 3, mRNA (cDNA clone MGC:169170 IMAGE:9021547), complete cds. // chr1 // 100 // 100 // 25 // 25 // 0 /// ENST00000521196 // ENSEMBL // cdna:known chromosome:GRCh37:11:86612:87605:-1 gene:ENSG00000224777 gene_biotype:pseudogene transcript_biotype:processed_transcript // chr1 // 76 // 68 // 13 // 17 // 0\tBC137547 // Q6IEY1\tENST00000426406 // Hs.632360 // muscle| normal /// ENST00000426406 // Hs.722724 // --- /// ENST00000332831 // Hs.632360 // muscle| normal /// ENST00000332831 // Hs.722724 // --- /// ENST00000456475 // Hs.632360 // muscle| normal /// ENST00000456475 // Hs.722724 // --- /// NM_001005277 // Hs.632360 // muscle| normal /// NM_001005224 // Hs.722724 // --- /// NM_001005504 // Hs.690459 // --- /// ENST00000320901 // Hs.690459 // --- /// BC137547 // Hs.632360 // muscle| normal /// BC137547 // Hs.722724 // ---\t---\tENST00000426406 // GO:0005886 // plasma membrane // traceable author statement /// ENST00000426406 // GO:0016021 // integral to membrane // inferred from electronic annotation /// ENST00000332831 // GO:0005886 // plasma membrane // traceable author statement /// ENST00000332831 // GO:0016021 // integral to membrane // inferred from electronic annotation /// ENST00000456475 // GO:0005886 // plasma membrane // traceable author statement /// ENST00000456475 // GO:0016021 // integral to membrane // inferred from electronic annotation /// NM_001005221 // GO:0005886 // plasma membrane // traceable author statement /// NM_001005221 // GO:0016021 // integral to membrane // inferred from electronic annotation /// NM_001005504 // GO:0005886 // plasma membrane // traceable author statement /// NM_001005504 // GO:0016021 // integral to membrane // inferred from electronic annotation /// ENST00000320901 // GO:0005886 // plasma membrane // traceable author statement /// ENST00000320901 // GO:0016021 // integral to membrane // inferred from electronic annotation /// BC137547 // GO:0005886 // plasma membrane // traceable author statement /// BC137547 // GO:0016021 // integral to membrane // inferred from electronic annotation\tENST00000426406 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// ENST00000426406 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation /// ENST00000332831 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// ENST00000332831 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation /// ENST00000456475 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// ENST00000456475 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation /// NM_001005221 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// NM_001005221 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation /// NM_001005504 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// NM_001005504 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation /// ENST00000320901 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// ENST00000320901 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation /// BC137547 // GO:0004930 // G-protein coupled receptor activity // inferred from electronic annotation /// BC137547 // GO:0004984 // olfactory receptor activity // inferred from electronic annotation\t---\tENST00000426406 // Pfam // IPR000276 // GPCR, rhodopsin-like, 7TM /// ENST00000426406 // Pfam // IPR019424 // 7TM GPCR, olfactory receptor/chemoreceptor Srsx /// ENST00000332831 // Pfam // IPR000276 // GPCR, rhodopsin-like, 7TM /// ENST00000332831 // Pfam // IPR019424 // 7TM GPCR, olfactory receptor/chemoreceptor Srsx /// ENST00000456475 // Pfam // IPR000276 // GPCR, rhodopsin-like, 7TM /// ENST00000456475 // Pfam // IPR019424 // 7TM GPCR, olfactory receptor/chemoreceptor Srsx /// ENST00000320901 // Pfam // IPR000276 // GPCR, rhodopsin-like, 7TM /// ENST00000320901 // Pfam // IPR019424 // 7TM GPCR, olfactory receptor/chemoreceptor Srsx\t3\tmain\t\tENST00000426406\n", "16657476\t16657476\tchr1\t+\t459656\t461954\t27\tENST00000424587 // LOC100508047 // uncharacterized LOC100508047 // --- // 100508047\tTCONS_00000121-XLOC_000003 // Rinn lincRNA // linc-SAMD11-9 chr1:+:459655-461954 // chr1 // 100 // 100 // 27 // 27 // 0 /// TCONS_00000442-XLOC_000663 // Rinn lincRNA // linc-ZNF692-2 chr1:-:521368-523833 // chr1 // 96 // 100 // 26 // 27 // 0 /// TCONS_l2_00002380-XLOC_l2_000720 // Broad TUCP // linc-ZNF692-5 chr1:-:235855-267253 // chr1 // 61 // 67 // 11 // 18 // 0 /// ENST00000424587 // ENSEMBL // cdna:known chromosome:GRCh37:1:235856:267253:-1 gene:ENSG00000228463 gene_biotype:processed_transcript transcript_biotype:processed_transcript // chr1 // 61 // 67 // 11 // 18 // 0 /// ENST00000441866 // ENSEMBL // havana:lincRNA chromosome:GRCh37:1:459656:461954:1 gene:ENSG00000236743 gene_biotype:lincRNA transcript_biotype:lincRNA // chr1 // 100 // 100 // 27 // 27 // 0 /// ENST00000417636 // ENSEMBL // havana:lincRNA chromosome:GRCh37:1:521369:523833:-1 gene:ENSG00000231709 gene_biotype:lincRNA transcript_biotype:lincRNA // chr1 // 96 // 100 // 26 // 27 // 0\t---\t---\t---\t---\t---\t---\t---\t3\tmain\t\tENST00000424587\n", "16657480\t16657480\tchr1\t+\t523009\t532878\t12\t---\tTCONS_00000124-XLOC_000004 // Rinn lincRNA // linc-SAMD11-8 chr1:+:529832-530595 // chr1 // 100 // 50 // 6 // 6 // 0\t---\t---\t---\t---\t---\t---\t---\t1\tmain\t\tTCONS_00000124-XLOC_000004\n" ] } ], "source": [ "# 1. First get the file paths using geo_get_relevant_filepaths function\n", "soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n", "\n", "# 2. Inspect the SOFT file structure to understand the annotation format\n", "# Read the first few lines of the SOFT file to examine its structure\n", "import gzip\n", "print(\"Preview of SOFT file content:\")\n", "with gzip.open(soft_file, 'rt') as f:\n", " for i, line in enumerate(f):\n", " print(line.strip())\n", " if i >= 20: # Print first 20 lines to understand structure\n", " break\n", "print(\"...\\n\")\n", "\n", "# 3. Try different approaches to extract gene annotation data\n", "# First, let's try the default method to see what's actually in the file\n", "gene_annotation = get_gene_annotation(soft_file)\n", "print(\"Gene annotation dataframe using default method:\")\n", "print(f\"Shape: {gene_annotation.shape}\")\n", "print(f\"Columns: {gene_annotation.columns.tolist()}\")\n", "print(gene_annotation.head(3))\n", "\n", "# 4. Check if there's another section in the file that might contain the mapping\n", "# Look for platform annotation information in the SOFT file\n", "print(\"\\nSearching for platform annotation section in SOFT file...\")\n", "with gzip.open(soft_file, 'rt') as f:\n", " platform_lines = []\n", " capture = False\n", " for i, line in enumerate(f):\n", " if \"^PLATFORM\" in line:\n", " capture = True\n", " platform_lines.append(line.strip())\n", " elif capture and line.startswith(\"!platform_table_begin\"):\n", " platform_lines.append(line.strip())\n", " for j in range(10): # Capture the next 10 lines to understand the table structure\n", " try:\n", " platform_line = next(f).strip()\n", " platform_lines.append(platform_line)\n", " except StopIteration:\n", " break\n", " break\n", " \n", " print(\"\\n\".join(platform_lines))\n", "\n", "# Maintain gene availability status as True based on previous steps\n", "is_gene_available = True\n" ] }, { "cell_type": "markdown", "id": "90fe5b9a", "metadata": {}, "source": [ "### Step 6: Gene Identifier Mapping" ] }, { "cell_type": "code", "execution_count": 7, "id": "9adb713f", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:41:44.466677Z", "iopub.status.busy": "2025-03-25T03:41:44.466557Z", "iopub.status.idle": "2025-03-25T03:41:45.316559Z", "shell.execute_reply": "2025-03-25T03:41:45.316123Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "Sample of the gene mapping dataframe:\n", " ID Gene\n", "0 16657436 NR_046018 // DDX11L1 // DEAD/H (Asp-Glu-Ala-As...\n", "1 16657440 ENST00000473358 // MIR1302-11 // microRNA 1302...\n", "2 16657445 NM_001005484 // OR4F5 // olfactory receptor, f...\n", "3 16657447 ---\n", "4 16657450 AK302511 // LOC100132062 // uncharacterized LO...\n", "Shape of mapping dataframe: (53617, 2)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\n", "After mapping to gene symbols:\n", "Gene expression data dimensions: 81076 genes × 60 samples\n", "\n", "Sample of gene expression data (first 5 genes, first 3 samples):\n", " GSM4800737 GSM4800738 GSM4800739\n", "Gene \n", "A- 12.128679 12.520490 12.287928\n", "A-2 1.807653 1.736914 1.684175\n", "A-52 3.715036 3.666027 3.689625\n", "A-E 1.212786 0.902884 1.320547\n", "A-I 3.026220 2.757676 2.957934\n" ] } ], "source": [ "# 1. From the gene annotation preview, we need to determine which columns to use\n", "# Looking at the gene annotation data, we can see:\n", "# - The 'ID' column contains the probe identifiers (e.g., 16657436) which match our gene expression data\n", "# - The 'gene_assignment' column appears to contain gene symbols and other gene information\n", "\n", "# 2. Extract the mapping information from the annotation dataframe\n", "# We need the ID column (probe identifiers) and gene_assignment column (which contains gene names)\n", "mapping_df = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='gene_assignment')\n", "\n", "# Print a sample of the mapping dataframe to verify\n", "print(\"\\nSample of the gene mapping dataframe:\")\n", "print(mapping_df.head())\n", "print(f\"Shape of mapping dataframe: {mapping_df.shape}\")\n", "\n", "# 3. Apply the gene mapping to convert probe-level measurements to gene expression data\n", "gene_data = apply_gene_mapping(expression_df=gene_data, mapping_df=mapping_df)\n", "\n", "# Print information about the resulting gene expression data\n", "print(\"\\nAfter mapping to gene symbols:\")\n", "print(f\"Gene expression data dimensions: {gene_data.shape[0]} genes × {gene_data.shape[1]} samples\")\n", "print(\"\\nSample of gene expression data (first 5 genes, first 3 samples):\")\n", "print(gene_data.iloc[:5, :3])\n", "\n", "# Maintain gene availability status\n", "is_gene_available = True if gene_data.shape[0] > 0 else False\n" ] }, { "cell_type": "markdown", "id": "574d2a13", "metadata": {}, "source": [ "### Step 7: Data Normalization and Linking" ] }, { "cell_type": "code", "execution_count": 8, "id": "9f5c8b0c", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:41:45.317883Z", "iopub.status.busy": "2025-03-25T03:41:45.317775Z", "iopub.status.idle": "2025-03-25T03:42:00.609190Z", "shell.execute_reply": "2025-03-25T03:42:00.608631Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Normalizing gene symbols...\n", "Gene data shape after normalization: 23274 genes × 60 samples\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Normalized gene expression data saved to ../../output/preprocess/Psoriasis/gene_data/GSE158448.csv\n", "Extracting clinical features from the original source...\n", "Extracted clinical features preview:\n", "{'GSM4800737': [0.0], 'GSM4800738': [0.0], 'GSM4800739': [0.0], 'GSM4800740': [0.0], 'GSM4800741': [0.0], 'GSM4800742': [1.0], 'GSM4800743': [1.0], 'GSM4800744': [1.0], 'GSM4800745': [1.0], 'GSM4800746': [1.0], 'GSM4800747': [1.0], 'GSM4800748': [1.0], 'GSM4800749': [1.0], 'GSM4800750': [1.0], 'GSM4800751': [1.0], 'GSM4800752': [1.0], 'GSM4800753': [1.0], 'GSM4800754': [1.0], 'GSM4800755': [1.0], 'GSM4800756': [1.0], 'GSM4800757': [1.0], 'GSM4800758': [1.0], 'GSM4800759': [1.0], 'GSM4800760': [1.0], 'GSM4800761': [1.0], 'GSM4800762': [1.0], 'GSM4800763': [1.0], 'GSM4800764': [1.0], 'GSM4800765': [1.0], 'GSM4800766': [1.0], 'GSM4800767': [1.0], 'GSM4800768': [1.0], 'GSM4800769': [1.0], 'GSM4800770': [1.0], 'GSM4800771': [1.0], 'GSM4800772': [1.0], 'GSM4800773': [1.0], 'GSM4800774': [1.0], 'GSM4800775': [1.0], 'GSM4800776': [1.0], 'GSM4800777': [1.0], 'GSM4800778': [1.0], 'GSM4800779': [1.0], 'GSM4800780': [1.0], 'GSM4800781': [1.0], 'GSM4800782': [1.0], 'GSM4800783': [1.0], 'GSM4800784': [1.0], 'GSM4800785': [1.0], 'GSM4800786': [1.0], 'GSM4800787': [1.0], 'GSM4800788': [1.0], 'GSM4800789': [1.0], 'GSM4800790': [1.0], 'GSM4800791': [1.0], 'GSM4800792': [1.0], 'GSM4800793': [1.0], 'GSM4800794': [1.0], 'GSM4800795': [1.0], 'GSM4800796': [1.0]}\n", "Clinical data shape: (1, 60)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Clinical features saved to ../../output/preprocess/Psoriasis/clinical_data/GSE158448.csv\n", "Linking clinical and genetic data...\n", "Linked data shape: (60, 23275)\n", "Handling missing values...\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Data shape after handling missing values: (60, 23275)\n", "\n", "Checking for bias in feature variables:\n", "For the feature 'Psoriasis', the least common label is '0.0' with 5 occurrences. This represents 8.33% of the dataset.\n", "The distribution of the feature 'Psoriasis' in this dataset is fine.\n", "\n", "A new JSON file was created at: ../../output/preprocess/Psoriasis/cohort_info.json\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Linked data saved to ../../output/preprocess/Psoriasis/GSE158448.csv\n", "Final dataset shape: (60, 23275)\n" ] } ], "source": [ "# 1. Check if gene data is available after mapping\n", "if gene_data.shape[0] == 0:\n", " print(\"Error: Gene expression matrix is empty after mapping.\")\n", " # Mark the dataset as not usable due to lack of gene expression data\n", " is_usable = validate_and_save_cohort_info(\n", " is_final=True,\n", " cohort=cohort,\n", " info_path=json_path,\n", " is_gene_available=False, # No usable gene data\n", " is_trait_available=True,\n", " is_biased=True,\n", " df=pd.DataFrame(),\n", " note=\"Failed to map probe IDs to gene symbols. The annotation format may not be compatible with the extraction methods.\"\n", " )\n", " print(\"Dataset deemed not usable due to lack of gene expression data.\")\n", "else:\n", " # Only proceed with normalization if we have gene data\n", " print(\"Normalizing gene symbols...\")\n", " gene_data_normalized = normalize_gene_symbols_in_index(gene_data)\n", " print(f\"Gene data shape after normalization: {gene_data_normalized.shape[0]} genes × {gene_data_normalized.shape[1]} samples\")\n", "\n", " # Save the normalized gene data\n", " os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)\n", " gene_data_normalized.to_csv(out_gene_data_file)\n", " print(f\"Normalized gene expression data saved to {out_gene_data_file}\")\n", " \n", " # Extract clinical features from the original data source\n", " print(\"Extracting clinical features from the original source...\")\n", " # Get background information and clinical data again\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", " # Extract clinical features\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,\n", " gender_row=gender_row,\n", " convert_gender=convert_gender\n", " )\n", " \n", " print(\"Extracted clinical features preview:\")\n", " print(preview_df(selected_clinical_df))\n", " print(f\"Clinical data shape: {selected_clinical_df.shape}\")\n", " \n", " # Save the extracted clinical features\n", " os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n", " selected_clinical_df.to_csv(out_clinical_data_file)\n", " print(f\"Clinical features saved to {out_clinical_data_file}\")\n", " \n", " # Link clinical and genetic data\n", " print(\"Linking clinical and genetic data...\")\n", " linked_data = geo_link_clinical_genetic_data(selected_clinical_df, gene_data_normalized)\n", " print(f\"Linked data shape: {linked_data.shape}\")\n", " \n", " # Check if the linked data has adequate data\n", " if linked_data.shape[0] == 0 or linked_data.shape[1] <= 4: # 4 is an arbitrary small number\n", " print(\"Error: Linked data has insufficient samples or features.\")\n", " is_usable = validate_and_save_cohort_info(\n", " is_final=True,\n", " cohort=cohort,\n", " info_path=json_path,\n", " is_gene_available=True,\n", " is_trait_available=True,\n", " is_biased=True,\n", " df=linked_data,\n", " note=\"Failed to properly link gene expression data with clinical features.\"\n", " )\n", " print(\"Dataset deemed not usable due to linking failure.\")\n", " else:\n", " # Handle missing values systematically\n", " print(\"Handling missing values...\")\n", " linked_data_clean = handle_missing_values(linked_data, trait_col=trait)\n", " print(f\"Data shape after handling missing values: {linked_data_clean.shape}\")\n", " \n", " # Check if there are still samples after missing value handling\n", " if linked_data_clean.shape[0] == 0:\n", " print(\"Error: No samples remain after handling missing values.\")\n", " is_usable = validate_and_save_cohort_info(\n", " is_final=True,\n", " cohort=cohort,\n", " info_path=json_path,\n", " is_gene_available=True,\n", " is_trait_available=True,\n", " is_biased=True,\n", " df=pd.DataFrame(),\n", " note=\"All samples were removed during missing value handling.\"\n", " )\n", " print(\"Dataset deemed not usable as all samples were filtered out.\")\n", " else:\n", " # Check if the dataset is biased\n", " print(\"\\nChecking for bias in feature variables:\")\n", " is_biased, linked_data_final = judge_and_remove_biased_features(linked_data_clean, trait)\n", " \n", " # Conduct final quality validation\n", " is_usable = validate_and_save_cohort_info(\n", " is_final=True,\n", " cohort=cohort,\n", " info_path=json_path,\n", " is_gene_available=True,\n", " is_trait_available=True,\n", " is_biased=is_biased,\n", " df=linked_data_final,\n", " note=\"Dataset contains gene expression data for Crohn's Disease patients, examining response to Infliximab treatment.\"\n", " )\n", " \n", " # Save linked data if usable\n", " if is_usable:\n", " os.makedirs(os.path.dirname(out_data_file), exist_ok=True)\n", " linked_data_final.to_csv(out_data_file)\n", " print(f\"Linked data saved to {out_data_file}\")\n", " print(f\"Final dataset shape: {linked_data_final.shape}\")\n", " else:\n", " print(\"Dataset deemed not usable for trait association studies, linked data not saved.\")" ] } ], "metadata": { "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.16" } }, "nbformat": 4, "nbformat_minor": 5 }