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