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MaayanLab/HarmonizomePythonScripts

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HarmonizomePythonScripts

The file containing all utility functions that are required to run the scripts can be found here: Utility Functions File

The file containing the gene symbol mapping (mapping all gene symbols to up-to-date human symbols) can be found here: Gene Symbol Mapping File

The file containing the gene-ID-to-symbol mappings can be found here: Gene ID to Symbol Mapping File

Resources: 41

Datasets: 116


Resource Data Set Genes Attributes Statistically Significant Associations Processing Script Processed Data
ARCHS4 Human Cell Line 23956 127 608457 ARCHS4 HCL Script ARCHS4 HCL Data
ARCHS4 Human Tissue 23169 108 500364 ARCHS4 HT Script ARCHS4 HT Data
ARCHS4 Human Kinase 17201 498 140739 ARCHS4 HK Script ARCHS4 HK Data
ARCHS4 Human Transcription Factors 21917 1724 470861 ARCHS4 HTF Script ARCHS4 HTF Data
ARCHS4 IDG Focused Genes 18020 352 95958 ARCHS4 IDG Script ARCHS4 IDG Data
Achilles Achilles 12279 216 2652264 Achilles Script Achilles Data
Allen Brain Atlas Adult Human Brain (RNA-Sequencing) 18629 100 92925 ABA-AHB-RS Script ABA-AHB-RS Data
Allen Brain Atlas Adult Human Brain (microarray) 18822 414 377048 ABA-AHB-MA Script ABA-AHB-MA Data
Allen Brain Atlas Aging Human Brain (RNA-Sequencing) Dementia TBI - Tissue 27858 32 55716 ABA-AB-D-TBI Script ABA-AB-D-TBI Data
Allen Brain Atlas Aging Human Brain (RNA-Sequencing) No Disease 28206 40 56388 ABA-AB-NS Script ABA-AB-NS Data
Allen Brain Atlas Developing Human Brain (RNA-Sequencing) Age 22411 31 44822 ABA-DB-RS-A Script ABA-DB-RS-A Data
Allen Brain Atlas Developing Human Brain (RNA-Sequencing) Sample 22411 524 587286 ABA-DB-RS-S Script ABA-DB-RS-S Data
Allen Brain Atlas Developing Human Brain (RNA-Sequencing) Tissue 22411 26 44822 ABA-DB-RS-T Script ABA-DB-RS-T Data
Allen Brain Atlas Developing Human Brain (microarray) Age 16827 27 27015 ABA-DB-MA-A Script ABA-DB-MA-A Data
Allen Brain Atlas Developing Human Brain (microarray) Sample 16827 492 413974 ABA-DB-MA-S Script ABA-DB-MA-S Data
Allen Brain Atlas Developing Human Brain (microarray) Tissue 16827 26 33653 ABA-DB-MA-T Script ABA-DB-MA-T Data
Allen Brain Atlas Prenatal Human Brain (microarray) Sample 19281 1198 1156878 ABA-P-S Script ABA-P-S Data
Allen Brain Atlas Prenatal Human Brain (microarray) Tissue 19281 516 501308 ABA-P-T Script ABA-P-T Data
BioGPS Cell Line 12296 93 228687 BGPS-CL Script BGPS-CL Data
BioGPS Tissue 16290 84 274099 BGPS-T Script BGPS-T Data
BioPlanet ABCA transporters in lipid homeostasis 9819 BioPlanet Scripts BioPlanet Data
BioPlex BioPlex 10824 10824 111694 BPLX Script BPLX Data
bgee Human Sample 34668 1077 14983142 BHS Script BHS Data
bgee Human Developmental Stage 34668 33 603839 BHDS Script BHDS Data
bgee Human Anatomical Entity 34668 308 4308050 BHAE Script BHAE Data
bgee Mouse Sample 16289 10797 9141706 BMS Script BMS Data
bgee Mouse Developmental Stage 16289 58 660778 BMDS Script BMDS Data
bgee Mouse Anatomical Entity 16289 3142 3163055 BMAE Script BMAE Data
bgee Rat Sample 15799 11 139136 BRS Script BRS Data
bgee Rat Developmental Stage 15799 2 22100 BRDS Script BRDS Data
bgee Rat Anatomical Entity 15799 10 132835 BRAE Script BRAE Data
CCLE Cell Line 17337 1036 898462 CCLE Script CCLE Data
Chip Atlas Chip Atlas 18539 963 1361218 CHPATLS Script CHPATLS Data
ClinVar ClinVar 1952 2934 6663 ClinVar Script ClinVar Data
CMAP CMAP 11801 200 142745 CMAP Script CMAP Data
CORUM CORUM 3753 2752 11280 CORUM Script CORUM Data
CTD Gene Chemical Interactions 15676 10366 160332 CTD-GCI Script CTD-GCI Data
CTD Gene Disease Interactions 17487 6384 22325153 CTD-GDI Script CTD-GDI Data
dbGAP dbGAP 3616 591 6088 dbGAP Script dbGAP Data
Drugbank Drug Carrier 61 270 352 DRGBNK-DC Script DRGBNK-DC Data
Drugbank Drug Enzyme 261 869 2429 DRGBNK-DE Script DRGBNK-DE Data
Drugbank Drug Target 2532 5108 13355 DRGBNK-DT Script DRGBNK-DT Data
Drugbank Drug Transporter 154 609 1784 DRGBNK-DTRS Script DRGBNK-DTRS Data
DSigDB Computational Drug Signatures 18215 15819 293199 DSigDB-CDS Script DSigDB-CDS Data
DSigDB FDA Approved Drugs 1279 1205 12571 DSigDB-FAD Script DSigDB-FAD Data
DSigDB Kinase Inhibitors 404 1150 16240 DSigDB-KI Script DSigDB-KI Data
DSigDB Perturbagen Signatures 10933 1163 158860 DSigDB-PS Script DSigDB-PS Data
ENCODE Transcription Factors 24656 456 1530489 ENCODE-TF Script ENCODE-TF Data
ENCODE Transcription Factors - Binding Sites 24656 1129 2220608 ENCODE-TF-BS Script ENCODE-TF-BS Data
ESCAPE ESCAPE 13514 44 81427 ESCAPE Script ESCAPE Data
GAD Gene-Disease Associations 14107 15522 109097 GAD Script GAD Data
GAD High Level Gene-Disease Associations 14120 19 42691 HL-GAD Script HL-GAD Data
GDSC Genomics of Drug Sensitivity in Cancer 12296 727 1787693 GDSC Script GDSC Data
GeneRIF GeneRIF 4368 125 9452 GeneRIF Script GeneRIF Data
GeneSigDB GeneSigDB 18534 3508 404516 GeneSigDB Script GeneSigDB Data
GO Biological Process 14481 11947 195513 GO-BP Script GO-BP Data
GO Cellular Component 12400 962 43458 GO-CC Script GO-CC Data
GO Molecular Function 11739 3618 48304 GO-uf Script GO-uf Data
GTEx Sample 25577 8555 10940561 GTEx Sample Script GTEx Sample Data
GTEx Tissue 25577 53 64221 GTEx Tissue Script GTEx Tissue Data
Guide to Pharmacology Chemical Ligands of Receptors 1577 7087 13759 GTP-CLR Tissue Script GTP-CLR Tissue Data
Guide to Pharmacology Protein Ligands of Receptors 224 196 427 GTP-PLR Script GTP-PLR Data
GWAS Catalog GWAS Catalog 6990 1978 18773 GWAS Catalog Script GWAS Catalog Data
GWASdb Disease 12091 225 60246 GWASdb Disease Script GWASdb Disease Data
GWASdb Phenotype 12652 487 70482 GWASdb Phenotype Script GWASdb Phenotype Data
hu.MAP hu.MAP 7669 7669 126176 hu.MAP Script hu.MAP Data
HPO Human Phenotype Ontology 3644 7841 415410 HPO Script HPO Data
Jensen Lab Compartments 18535 2826 829693 JL-C Script JL-C Data
Jensen Lab Disease 13149 3679 52079 JL-D Script JL-D Data
Jensen Lab Tissues 18565 4098 434311 JL-T Script JL-T Data
MGI Mouse Gene Ontology 7758 8639 134408 MGI Script MGI Data
miRTarBase miRTarBase 15575 3551 417884 miRTarBase Script miRTarBase Data
Pathway Commons Protein-Protein Interactions 16291 18511 1125042 PCPPI Script PCPPI Data
Pathway Commons Pathways 11164 51319 1257932 PCP Script PCP Data
PheWeb PheWeb 2716 PheWeb Scripts PheWeb Data
Reactome Reactome 10237 1887 105556 Reactome Script Reactome Data
Roadmap Epigenomics Cell and Tissue Expression 18375 57 209475 Roadmap Epigenomics Script Roadmap Epigenomics Data
TargetScanHuman TargetScanHuman 18028 2318 5898446 TargetScanHuman Script TargetScanHuman Data
TCGA Adrenocortical Carcinoma 18423 79 72970 TCGA-ACC Script TCGA-ACC Data
TCGA Bladder Urothelial Carcinoma 18549 430 398197 TCGA-BLCA Script TCGA-BLCA Data
TCGA Brain Lower Grade Glioma 18480 530 489769 TCGA-LGG Script TCGA-LGG Data
TCGA Breast Invasive Carcinoma 18511 1215 1124480 TCGA-BRCA Script TCGA-BRCA Data
TCGA Cervical squamous cell carcinoma and endocervical adenocarcinoma 18478 309 284538 TCGA-CESC Script TCGA-CESC Data
TCGA Cholangiocarcinoma 18589 45 41743 TCGA-CHOL Script TCGA-CHOL Data
TCGA Colon Adenocarcinoma 18340 501 459393 TCGA-COAD Script TCGA-COAD Data
TCGA Esophageal Carcinoma 18875 198 186087 TCGA-ESCA Script TCGA-ESCA Data
TCGA Glioblastoma Multiforme 18471 173 159910 TCGA-GBM Script TCGA-GBM Data
TCGA Head and Neck Squamous Cell Carcinoma 18648 566 527943 TCGA-HNSC Script TCGA-HNSC Data
TCGA Kidney Chromophobe 18540 91 84676 TCGA-KICH Script TCGA-KICH Data
TCGA Kidney Renal Clear Cell Carcinoma 18665 606 565628 TCGA-KIRC Script TCGA-KIRC Data
TCGA Kidney Renal Papillary Cell Carcinoma 18546 323 299781 TCGA-KIRP Script TCGA-KIRP Data
TCGA Liver Hepatocellular Carcinoma 18339 423 387737 TCGA-LIHC Script TCGA-LIHC Data
TCGA Lung Adenocarcinoma 18508 577 533911 TCGA-LUAD Script TCGA-LUAD Data
TCGA Lung Squamous Cell Carcinoma 18608 552 513287 TCGA-LUSC Script TCGA-LUSC Data
TCGA Lymphoid Neoplasm Diffuse Large B-cell Lymphoma 18967 48 42973 TCGA-DLBC Script TCGA-DLBC Data
TCGA Mesothelioma 18545 87 81072 TCGA-MESO Script TCGA-MESO Data
TCGA Ovarian Serous Cystadenocarcinoma 18621 429 399505 TCGA-OV Script TCGA-OV Data
TCGA Pancreatic Adenocarcinoma 18493 183 169642 TCGA-PAAD Script TCGA-PAAD Data
TCGA Pheochromocytoma and Paraganglioma 18370 187 172133 TCGA-PCPG Script TCGA-PCPG Data
TCGA Prostate Adenocarcinoma 18528 550 509464 TCGA-PRAD Script TCGA-PRAD Data
TCGA Rectum Adenocarcinoma 18335 177 162528 TCGA-READ Script TCGA-READ Data
TCGA Sarcoma 18584 265 245886 TCGA-SARC Script TCGA-SARC Data
TCGA Skin Cutaneous Melanoma 18612 473 439949 TCGA-SKCM Script TCGA-SKCM Data
TCGA Stomach Adenocarcinoma 18917 453 428467 TCGA-STAD Script TCGA-STAD Data
TCGA Testicular Germ Cell Tumors 18742 156 145048 TCGA-TGCT Script TCGA-TGCT Data
TCGA Thymoma 18514 122 112695 TCGA-THYM Script TCGA-THYM Data
TCGA Thyroid Carcinoma 18371 572 525419 TCGA-THCA Script TCGA-THCA Data
TCGA Uterine Carcinosarcoma 18821 57 56384 TCGA-UCS Script TCGA-UCS Data
TCGA Uterine Corpus Endometrial Carcinoma 18689 581 542785 TCGA-UCEC Script TCGA-UCEC Data
TCGA Uveal Melanoma 18136 80 73121 TCGA-UVM Script TCGA-UVM Data
The Human Metabolome Database HMDB 5309 22128 848829 TCGA-HMDB Script TCGA-HMDB Data
The Human Protein Atlas Celline (RNA-seq) 17661 56 197848 THPA-CL-RS Script THPA-CL-RS Data
The Human Protein Atlas Normal Tissue (immunohistochemisty) 9490 108 117708 THPA-NT-I Script THPA-NT-I Data
The Human Protein Atlas Normal Tissue (RNA-seq) 18200 37 134717 THPA-NT-RS Script THPA-NT-RS Data
UK BioBank MedicationCategory-Gene Associations 1212 20 2338 UKBioBankGWAS Script UKBioBankGWAS Data
WikiPathways WikiPathways 5388 372 15503 WikiPathways Script WikiPathways Data

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