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{
"cells": [
{
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"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 = \"Depression\"\n",
"cohort = \"GSE138297\"\n",
"\n",
"# Input paths\n",
"in_trait_dir = \"../../input/GEO/Depression\"\n",
"in_cohort_dir = \"../../input/GEO/Depression/GSE138297\"\n",
"\n",
"# Output paths\n",
"out_data_file = \"../../output/preprocess/Depression/GSE138297.csv\"\n",
"out_gene_data_file = \"../../output/preprocess/Depression/gene_data/GSE138297.csv\"\n",
"out_clinical_data_file = \"../../output/preprocess/Depression/clinical_data/GSE138297.csv\"\n",
"json_path = \"../../output/preprocess/Depression/cohort_info.json\"\n"
]
},
{
"cell_type": "markdown",
"id": "76a5e5ab",
"metadata": {},
"source": [
"### Step 1: Initial Data Loading"
]
},
{
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"id": "cf9540f1",
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"execution": {
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Background Information:\n",
"!Series_title\t\"The host response of IBS patients to allogenic and autologous faecal microbiota transfer\"\n",
"!Series_summary\t\"In this randomised placebo-controlled trial, irritable bowel syndrome (IBS) patients were treated with faecal material from a healthy donor (n=8, allogenic FMT) or with their own faecal microbiota (n=8, autologous FMT). The faecal transplant was administered by whole colonoscopy into the caecum (30 g of stool in 150 ml sterile saline). Two weeks before the FMT (baseline) as well as two and eight weeks after the FMT, the participants underwent a sigmoidoscopy, and biopsies were collected at a standardised location (20-25 cm from the anal verge at the crossing with the arteria iliaca communis) from an uncleansed sigmoid. In patients treated with allogenic FMT, predominantly immune response-related genes sets were induced, with the strongest response two weeks after FMT. In patients treated with autologous FMT, predominantly metabolism-related gene sets were affected.\"\n",
"!Series_overall_design\t\"Microarray analysis was performed on sigmoid biopsies from ucleansed colon at baseline, 2 weeks and 8 weeks after FMT .\"\n",
"Sample Characteristics Dictionary:\n",
"{0: ['tissue: uncleansed colon'], 1: ['sex (female=1, male=0): 1', 'sex (female=1, male=0): 0'], 2: ['subjectid: 1', 'subjectid: 2', 'subjectid: 3', 'subjectid: 4', 'subjectid: 5', 'subjectid: 6', 'subjectid: 7', 'subjectid: 8', 'subjectid: 10', 'subjectid: 11', 'subjectid: 12', 'subjectid: 13', 'subjectid: 14', 'subjectid: 15', 'subjectid: 16'], 3: ['age (yrs): 49', 'age (yrs): 21', 'age (yrs): 31', 'age (yrs): 59', 'age (yrs): 40', 'age (yrs): 33', 'age (yrs): 28', 'age (yrs): 36', 'age (yrs): 50', 'age (yrs): 27', 'age (yrs): 23', 'age (yrs): 32', 'age (yrs): 38'], 4: ['moment of sampling (pre/post intervention): Baseline (app. 2w before intervention)', 'moment of sampling (pre/post intervention): 2 weeks after intervention', 'moment of sampling (pre/post intervention): 8 weeks after intervention'], 5: ['time of sampling: Morning, after overnight fasting'], 6: ['experimental condition: Allogenic FMT', 'experimental condition: Autologous FMT']}\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": "2e7fba49",
"metadata": {},
"source": [
"### Step 2: Dataset Analysis and Clinical Feature Extraction"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "8e76850c",
"metadata": {
"execution": {
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"outputs": [
{
"data": {
"text/plain": [
"False"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Get the necessary libraries\n",
"import pandas as pd\n",
"import os\n",
"import json\n",
"from typing import Callable, Dict, Any, Optional\n",
"\n",
"# 1. Gene Expression Data Availability\n",
"# Based on the background information, the dataset contains microarray analysis data\n",
"# Microarray analysis typically produces gene expression data, so this is likely gene expression data\n",
"is_gene_available = True\n",
"\n",
"# 2. Variable Availability and Data Type Conversion\n",
"# 2.1 Data Availability\n",
"# For trait (Depression), we need to see if there's a relevant field in the sample characteristics\n",
"# Looking at the data, there's no explicit \"Depression\" field, but we may infer it from \"experimental condition\"\n",
"# The study is about IBS (Irritable Bowel Syndrome) patients, not depression\n",
"trait_row = None # Depression data is not available in this IBS study\n",
"\n",
"# Age data is available at index 3\n",
"age_row = 3\n",
"\n",
"# Gender data is available at index 1\n",
"gender_row = 1\n",
"\n",
"# 2.2 Data Type Conversion\n",
"# For trait (Depression) - Not applicable as data is not available\n",
"def convert_trait(value):\n",
" return None\n",
"\n",
"# For age - Convert to continuous value\n",
"def convert_age(value):\n",
" if value is None:\n",
" return None\n",
" try:\n",
" # Extract the numeric part after the colon\n",
" age_str = value.split(':')[1].strip()\n",
" return float(age_str)\n",
" except (ValueError, IndexError):\n",
" return None\n",
"\n",
"# For gender - Convert to binary (female=0, male=1)\n",
"def convert_gender(value):\n",
" if value is None:\n",
" return None\n",
" try:\n",
" # The format is already \"sex (female=1, male=0): X\"\n",
" # But we'll convert to our standard of female=0, male=1\n",
" gender_str = value.split(':')[1].strip()\n",
" # Flip the values because in our standard female=0, male=1\n",
" return 1 - int(gender_str)\n",
" except (ValueError, IndexError):\n",
" return None\n",
"\n",
"# 3. Save Metadata\n",
"# Conduct initial filtering on the usability of the dataset\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",
"# Skip this step as trait_row is None, indicating clinical data for the trait is not available\n"
]
},
{
"cell_type": "markdown",
"id": "72c933eb",
"metadata": {},
"source": [
"### Step 3: Gene Data Extraction"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "94968d87",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T08:37:29.209500Z",
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"shell.execute_reply": "2025-03-25T08:37:29.480860Z"
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},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Matrix file found: ../../input/GEO/Depression/GSE138297/GSE138297_series_matrix.txt.gz\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"Gene data shape: (53617, 45)\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"
]
}
],
"source": [
"# 1. Get the SOFT and matrix file paths again \n",
"soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n",
"print(f\"Matrix file found: {matrix_file}\")\n",
"\n",
"# 2. Use the get_genetic_data function from the library to get the gene_data\n",
"try:\n",
" gene_data = get_genetic_data(matrix_file)\n",
" print(f\"Gene data shape: {gene_data.shape}\")\n",
" \n",
" # 3. Print the first 20 row IDs (gene or probe identifiers)\n",
" print(\"First 20 gene/probe identifiers:\")\n",
" print(gene_data.index[:20])\n",
"except Exception as e:\n",
" print(f\"Error extracting gene data: {e}\")\n"
]
},
{
"cell_type": "markdown",
"id": "0a13b62d",
"metadata": {},
"source": [
"### Step 4: Gene Identifier Review"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "ba8172bd",
"metadata": {
"execution": {
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"outputs": [],
"source": [
"# Based on the gene identifiers seen in the previous output, these appear to be probe identifiers \n",
"# (possibly from an Illumina or Affymetrix microarray) rather than standard human gene symbols.\n",
"# The identifiers shown (like '16650001', '16650003', etc.) are numeric and don't match the \n",
"# conventional format of human gene symbols (e.g., BRCA1, TP53).\n",
"\n",
"# These identifiers will need to be mapped to standard gene symbols for meaningful analysis.\n",
"\n",
"requires_gene_mapping = True\n"
]
},
{
"cell_type": "markdown",
"id": "b0f5427b",
"metadata": {},
"source": [
"### Step 5: Gene Annotation"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "87ba06e8",
"metadata": {
"execution": {
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Platform title found: [HuGene-2_1-st] Affymetrix Human Gene 2.1 ST Array [transcript (gene) version]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Gene annotation preview:\n",
"{'ID': ['16657436', '16657440', '16657445', '16657447', '16657450', '16657469', '16657473', '16657476', '16657480', '16657485'], 'probeset_id': ['16657436', '16657440', '16657445', '16657447', '16657450', '16657469', '16657473', '16657476', '16657480', '16657485'], 'seqname': ['chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1', 'chr1'], 'strand': ['+', '+', '+', '+', '+', '+', '+', '+', '+', '+'], 'start': ['12190', '29554', '69091', '160446', '317811', '329790', '367640', '459656', '523009', '557143'], 'stop': ['13639', '31109', '70008', '161525', '328581', '342507', '368634', '461954', '532878', '566063'], 'total_probes': [25.0, 28.0, 8.0, 13.0, 36.0, 27.0, 25.0, 27.0, 12.0, 13.0], 'gene_assignment': ['NR_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 // --- // ---', 'ENST00000473358 // 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', 'NM_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', '---', 'AK302511 // 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', 'BC118988 // 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', 'ENST00000426406 // 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', 'ENST00000424587 // LOC100508047 // uncharacterized LOC100508047 // --- // 100508047', '---', 'XR_132471 // MTND2P28 // MT-ND2 pseudogene 28 // --- // 100652939 /// XR_133228 // LOC100653240 // NADH-ubiquinone oxidoreductase chain 2-like // --- // 100653240'], 'mrna_assignment': ['NR_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', 'ENST00000473358 // ENSEMBL // cdna:known chromosome:GRCh37:1:29554:31097:1 gene:ENSG00000243485 gene_biotype:antisense transcript_biotype:antisense // chr1 // 100 // 71 // 20 // 20 // 0', 'NM_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', 'TCONS_00000119-XLOC_000001 // Rinn lincRNA // linc-OR4F16-10 chr1:+:160445-161525 // chr1 // 100 // 100 // 13 // 13 // 0', 'AK302511 // 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', 'BC118988 // 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', 'ENST00000426406 // 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', 'TCONS_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', 'TCONS_00000124-XLOC_000004 // Rinn lincRNA // linc-SAMD11-8 chr1:+:529832-530595 // chr1 // 100 // 50 // 6 // 6 // 0', 'XR_132471 // RefSeq // PREDICTED: Homo sapiens NADH-ubiquinone oxidoreductase chain 2-like (LOC100652939), miscRNA. // chr1 // 100 // 77 // 10 // 10 // 0 /// XR_133228 // RefSeq // PREDICTED: Homo sapiens NADH-ubiquinone oxidoreductase chain 2-like (LOC100653240), miscRNA. // chr1 // 100 // 31 // 4 // 4 // 0'], 'swissprot': ['NR_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', '---', '---', '---', 'AK302511 // 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', '---', 'BC137547 // Q6IEY1', '---', '---', '---'], 'unigene': ['NR_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', '---', 'NM_001005484 // Hs.554500 // --- /// ENST00000335137 // Hs.554500 // ---', '---', 'AK302511 // 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', '---', 'ENST00000426406 // 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 // ---', '---', '---', '---'], 'GO_biological_process': ['---', '---', '---', '---', '---', '---', '---', '---', '---', '---'], 'GO_cellular_component': ['---', '---', 'NM_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', '---', '---', '---', 'ENST00000426406 // 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', '---', '---', '---'], 'GO_molecular_function': ['---', '---', 'NM_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', '---', '---', '---', 'ENST00000426406 // 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', '---', '---', '---'], 'pathway': ['---', '---', '---', '---', '---', '---', '---', '---', '---', '---'], 'protein_domains': ['---', '---', 'ENST00000335137 // Pfam // IPR000276 // GPCR, rhodopsin-like, 7TM /// ENST00000335137 // Pfam // IPR019424 // 7TM GPCR, olfactory receptor/chemoreceptor Srsx', '---', '---', '---', 'ENST00000426406 // 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', '---', '---', '---'], 'crosshyb_type': ['3', '3', '3', '3', '3', '3', '3', '3', '1', '1'], 'category': ['main', 'main', 'main', 'main', 'main', 'main', 'main', 'main', 'main', 'main'], 'GB_ACC': ['NR_046018', nan, 'NM_001005484', nan, 'AK302511', 'BC118988', nan, nan, nan, 'XR_132471'], 'SPOT_ID': [nan, 'ENST00000473358', nan, 'TCONS_00000119-XLOC_000001', nan, nan, 'ENST00000426406', 'ENST00000424587', 'TCONS_00000124-XLOC_000004', nan]}\n"
]
}
],
"source": [
"# 1. Use the 'get_gene_annotation' function from the library to get gene annotation data from the SOFT file.\n",
"gene_annotation = get_gene_annotation(soft_file)\n",
"\n",
"# Check if there are any platforms defined in the SOFT file that might contain annotation data\n",
"with gzip.open(soft_file, 'rt') as f:\n",
" soft_content = f.read()\n",
"\n",
"# Look for platform sections in the SOFT file\n",
"platform_sections = re.findall(r'^!Platform_title\\s*=\\s*(.+)$', soft_content, re.MULTILINE)\n",
"if platform_sections:\n",
" print(f\"Platform title found: {platform_sections[0]}\")\n",
"\n",
"# Try to extract more annotation data by reading directly from the SOFT file\n",
"# Look for lines that might contain gene symbol mappings\n",
"symbol_pattern = re.compile(r'ID_REF\\s+Symbol|ID\\s+Gene Symbol', re.IGNORECASE)\n",
"annotation_lines = []\n",
"with gzip.open(soft_file, 'rt') as f:\n",
" for line in f:\n",
" if symbol_pattern.search(line):\n",
" annotation_lines.append(line)\n",
" # Collect the next few lines to see the annotation structure\n",
" for _ in range(10):\n",
" annotation_lines.append(next(f, ''))\n",
"\n",
"if annotation_lines:\n",
" print(\"Found potential gene symbol mappings:\")\n",
" for line in annotation_lines:\n",
" print(line.strip())\n",
"\n",
"# 2. Use the 'preview_df' function from the library to preview the data and print out the results.\n",
"print(\"\\nGene annotation preview:\")\n",
"print(preview_df(gene_annotation, n=10))\n",
"\n",
"# If we need an alternative source of mapping, check if there are any other annotation files in the cohort directory\n",
"cohort_files = os.listdir(in_cohort_dir)\n",
"annotation_files = [f for f in cohort_files if 'annotation' in f.lower() or 'platform' in f.lower()]\n",
"if annotation_files:\n",
" print(\"\\nAdditional annotation files found in the cohort directory:\")\n",
" for file in annotation_files:\n",
" print(file)\n"
]
},
{
"cell_type": "markdown",
"id": "7f8fcb67",
"metadata": {},
"source": [
"### Step 6: Gene Identifier Mapping"
]
},
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Mapping dataframe preview (first 5 rows):\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"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Original gene expression data shape (before mapping): (23274, 45)\n",
"Number of unique genes after mapping: 23274\n",
"\n",
"First 5 genes and their expression values:\n",
" GSM4104672 GSM4104673 GSM4104674 GSM4104675 GSM4104676 \\\n",
"Gene \n",
"A1BG 2.936132 2.803615 3.018072 2.549726 3.007617 \n",
"A1BG-AS1 1.384362 1.206311 1.430827 1.284927 1.401303 \n",
"A1CF 2.981835 2.945819 2.857161 2.967612 2.899801 \n",
"A2M 3.467480 3.621222 3.498609 3.411768 3.649466 \n",
"A2M-AS1 1.494063 1.592554 1.615310 1.529224 1.728269 \n",
"\n",
" GSM4104677 GSM4104678 GSM4104679 GSM4104680 GSM4104681 ... \\\n",
"Gene ... \n",
"A1BG 2.708221 2.533589 2.791591 3.039732 2.808330 ... \n",
"A1BG-AS1 1.308060 1.106003 1.233850 1.264744 1.370906 ... \n",
"A1CF 2.844060 2.943882 3.044562 2.744889 2.856325 ... \n",
"A2M 3.210363 3.289232 3.379433 3.156047 3.489444 ... \n",
"A2M-AS1 1.298303 1.297931 1.414137 1.198760 1.510490 ... \n",
"\n",
" GSM4104707 GSM4104708 GSM4104709 GSM4104710 GSM4104711 \\\n",
"Gene \n",
"A1BG 2.799853 2.756029 2.829148 2.957482 2.464350 \n",
"A1BG-AS1 1.264744 1.220920 1.294038 1.264744 1.227988 \n",
"A1CF 2.760791 2.943351 2.944030 2.949854 2.920951 \n",
"A2M 3.413081 3.480970 3.549215 3.279434 3.346983 \n",
"A2M-AS1 1.411210 1.460752 1.523808 1.388862 1.375982 \n",
"\n",
" GSM4104712 GSM4104713 GSM4104714 GSM4104715 GSM4104716 \n",
"Gene \n",
"A1BG 2.645806 2.846628 2.922873 3.053455 2.925770 \n",
"A1BG-AS1 1.311749 1.174100 1.277915 1.359687 1.345724 \n",
"A1CF 2.899335 2.861309 2.838252 2.868343 2.852788 \n",
"A2M 3.403498 3.496903 3.444789 3.653379 3.544460 \n",
"A2M-AS1 1.435430 1.508184 1.428202 1.597353 1.487036 \n",
"\n",
"[5 rows x 45 columns]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Gene expression data saved to: ../../output/preprocess/Depression/gene_data/GSE138297.csv\n"
]
}
],
"source": [
"# 1. Looking at the gene identifiers and the annotation data\n",
"# The gene expression data has identifiers like '16650001', '16650003', etc.\n",
"# In the gene annotation data, we see the 'ID' column matches this format\n",
"\n",
"# 2. Extract the mapping between ID (probe) and gene symbols\n",
"# Looking at the gene_assignment column, we need to extract proper gene symbols from strings \n",
"# like \"NR_046018 // DDX11L1 // DEAD/H...\"\n",
"prob_col = 'ID'\n",
"gene_col = 'gene_assignment'\n",
"mapping_df = get_gene_mapping(gene_annotation, prob_col, gene_col)\n",
"\n",
"# Print the first few rows of the mapping dataframe to verify\n",
"print(\"Mapping dataframe preview (first 5 rows):\")\n",
"print(mapping_df.head())\n",
"\n",
"# 3. Apply the gene mapping to convert probe-level measurements to gene-level data\n",
"# This function will extract human gene symbols from the complex gene_assignment text,\n",
"# handle many-to-many relationships, and aggregate data by gene\n",
"gene_data = apply_gene_mapping(gene_data, mapping_df)\n",
"\n",
"# Normalize gene symbols to handle synonyms and variations\n",
"gene_data = normalize_gene_symbols_in_index(gene_data)\n",
"\n",
"# Print information about the resulting gene expression dataframe\n",
"print(f\"\\nOriginal gene expression data shape (before mapping): {gene_data.shape}\")\n",
"print(f\"Number of unique genes after mapping: {len(gene_data.index.unique())}\")\n",
"\n",
"# Preview the first few genes and their expression values\n",
"print(\"\\nFirst 5 genes and their expression values:\")\n",
"print(gene_data.head())\n",
"\n",
"# Save the gene data to a file for future use\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\"\\nGene expression data saved to: {out_gene_data_file}\")\n"
]
},
{
"cell_type": "markdown",
"id": "ba3152ad",
"metadata": {},
"source": [
"### Step 7: Data Normalization and Linking"
]
},
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"id": "3c91153f",
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"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"No Depression data available in this dataset.\n",
"Abnormality detected in the cohort: GSE138297. Preprocessing failed.\n",
"Dataset is not usable for Depression analysis. No linked data file saved.\n"
]
}
],
"source": [
"# 1. We'll normalize gene symbols in the gene expression data\n",
"# Note: We've already done this in step 6, so we can skip this part\n",
"\n",
"# 2. Link the clinical and genetic data\n",
"# Based on step 2, we confirmed that this dataset does not contain Depression data\n",
"# It's an IBS (Irritable Bowel Syndrome) study, not a Depression study\n",
"trait_row = None # Depression data is not available in this IBS study\n",
"\n",
"# Since trait data is not available, we can't proceed with clinical data extraction\n",
"print(f\"No {trait} data available in this dataset.\")\n",
"\n",
"# Create a minimal dataframe with the trait column (though empty)\n",
"minimal_df = pd.DataFrame(columns=[trait])\n",
"\n",
"# 5. Validate and save cohort information to record that this dataset is not usable for our purposes\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=False, # No trait data available\n",
" is_biased=False, # Provide a boolean value instead of None\n",
" df=minimal_df, # Provide a minimal dataframe with trait column\n",
" note=\"Dataset is about IBS patients, not Depression. The study was about faecal microbiota transfer in IBS patients.\"\n",
")\n",
"\n",
"# 6. Since the data is not usable for our Depression study, we don't save linked data\n",
"print(\"Dataset is not usable for Depression analysis. No linked data file saved.\")"
]
}
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|