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 58,433 transcripts.

Predictions are based on gene expression profiles of 29,138 samples.

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	4205
Gene Ontology - Molecular Function	855
Gene Ontology - Cellular Component	532
REACTOME	658
KEGG	186
BIOCARTA	213
Chemical and Genetic Perturbations	2976
Transcription Factor Targets	571
MicroRNA Targets	205
Hallmark Gene Sets	50
Cancer Gene Neighborhoods	427
Cancer Modules	414
Oncogenic Signatures	189
Immunologic Signatures	4872
Mammalian Phenotypes MGI	4071
HPO Ontology	3135

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 /// RNAseq 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