Supporting publication available at Nature Communications : Link to paper CITATION: Urzua-Traslavina CG, Leeuwenburgh VC, Bhattacharya A, Loipfinger S, van Vugt MATM, de Vries EGE, Fehrmann RSN. Improving gene function predictions using independent transcriptional components. Nat Commun. 2021 Mar 5;12(1):1464. doi: 10.1038/s41467-021-21671-w. PMID: 33674610; PMCID: PMC7935959.

Predictions available for 19,635 genes.

Predictions are based on gene expression profiles of 106,462 sample.

These samples represent many tissue types, disease states, cellular contexts, experimental variation and therapeutic/chemical perturbations.

Gene set database	Number of gene sets included
Gene Ontology - Biological Process (MSigDB v6.2)	4203
Gene Ontology - Molecular Function (MSigDB v6.2)	843
Gene Ontology - Cellular Component (MSigDB v6.2)	528
REACTOME (MSigDB v6.2)	645
KEGG (MSigDB v6.2)	185
BIOCARTA (MSigDB v6.2)	210
Chemical and Genetic Perturbations (CGP MSigDB v6.2)	2968
Transcription Factor Targets (TFT MSigDB v6.2)	573
MicroRNA Targets (MIR MSigDB v6.2)	205
Hallmark Gene Sets (MSigDB v6.2)	50
Cancer Gene Neighborhoods (CGN MSigDB v6.2)	427
Cancer Modules (CM MSigDB v6.2)	427
Oncogenic Signatures (MSigDB v6.2)	189
Immunologic Signatures (MSigDB v6.2)	4872
Mammalian Phenotypes (MGI April 2018)	4004
Human Phenotype Ontology (April 2018)	3100

Precompiled version for the mac OS (11.1) of Analyertool 5 (to run first install QT version 5.15.1): link - README

For question, contact me at r.s.n.fehrmann@umcg.nl

Also see my website at: www.rudolffehrmann.nl

Support data for GenetICA-Network /// Microarray version

Readme explaining content of files: link

consensus independent component results	Download links
consensus independent components	link
consensus mixing matrix	link
gene set definitions	Download links
gene set definitions: Gene Ontology - Biological Process (MSigDB v6.2)	link
gene set definitions: Gene Ontology - Molecular Function (MSigDB v6.2)	link
gene set definitions: Gene Ontology - Cellular Component (MSigDB v6.2)	link
gene set definitions: REACTOME (MSigDB v6.2)	link
gene set definitions: KEGG (MSigDB v6.2)	link
gene set definitions: BIOCARTA (MSigDB v6.2)	link
gene set definitions: Chemical and Genetic Perturbations (CGP MSigDB v6.2)	link
gene set definitions: Transcription Factor Targets (TFT MSigDB v6.2)	link
gene set definitions: MicroRNA Targets (MIR MSigDB v6.2)	link
gene set definitions: Hallmark Gene Sets (MSigDB v6.2)	link
gene set definitions: Cancer Gene Neighborhoods (CGN MSigDB v6.2)	link
gene set definitions: Cancer Modules (CM MSigDB v6.2)	link
gene set definitions: Oncogenic Signatures (MSigDB v6.2)	link
gene set definitions: Immunologic Signatures (MSigDB v6.2)	link
gene set definitions: Mammalian Phenotypes	link
gene set definitions: Human Phenotype Ontology	link
prediction scores for all gene/gene set combination	Download links
Hallmark	link
Oncogenic Signatures	link
BIOCARTA	link
KEGG	link
MicroRNA Targets	link
Cancer Gene Neighborhoods	link
Cancer Modules	link
REACTOME	link
Gene Ontology - Cellular Component	link
Gene Ontology - Molecular Function	link
Gene Ontology - Biological Process	link
Chemical and Genetic Pertubations	link
Transcription Factor Targets	link
Immunologic Signatures	link
Mammalian Phenotypes	link
Human Phenotype Ontology	link
mean vector of gene set members in consensus mixing matrix	Download links
Hallmark	link
Oncogenic Signatures	link
BIOCARTA	link
KEGG	link
MicroRNA Targets	link
Cancer Gene Neighborhoods	link
Cancer Modules	link
REACTOME	link
Gene Ontology - Cellular Component	link
Gene Ontology - Molecular Function	link
Gene Ontology - Biological Process	link
Chemical and Genetic Pertubations	link
Transcription Factor Targets	link
Immunologic Signatures	link
Mammalian Phenotypes	link
Human Phenotype Ontology	link