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Table 1 GMT files used for gene-list overlap analysis in L2N

From: Lists2Networks: Integrated analysis of gene/protein lists

Name

Description

Source

GMT File Creator

WikiPathways_pathways

Biological pathways

http://www.wikipathways.org

Ma'ayan lab

Reactome_pathways

Biological pathways

http://www.reactome.org

Ma'ayan lab

GenMAPP_patwhays

Biological pathways

http://www.genmapp.org

MSigDB

KEGG_pathways

Signaling pathways

http://www.genome.jp/kegg

MSigDB

BioCarta_pathways

Signaling pathways

http://www.biocarta.com

MSigDB

Chromosome_location

Chromosome location

http://genome.ucsc.edu

MSigDB

TFs_predicted_binidng_sites

TRANSFAC predicted sites

http://genome.ucsc.edu

Ma'ayan lab

TFs_chip_interactions

ChIP interactions collected from literature by the Ma'ayan lab

Various sources from individual publications

Ma'ayan lab

Gene_Ontology_BP

Gene Ontology Biological Process

http://www.geneontology.org

Ma'ayan lab

Gene_Ontology_MF

Gene Ontology Molecular Function

http://www.geneontology.org

Ma'ayan lab

Gene_Ontology_CC

Gene Ontology Cellular Component

http://www.geneontology.org

Ma'ayan lab

HMDB_metabolites

Genes associated with Metabolites

http://www.hmdb.ca

Ma'ayan lab

OMIM_disease_genes

Genes associated with a specific disease

http://www.ncbi.nlm.nih.gov/omim

Ma'ayan lab

OMIM_disease_neighborhoods

Genes associated with a specific disease expanded using protein interactions and the genes2networks algorithm

http://www.ncbi.nlm.nih.gov/omim and http://actin.pharm.mssm.edu/genes2networks

Ma'ayan lab

KEA_kinases

Substrates of protein kinases collected from different databases

http://amp.pharm.mssm.edu/lib/kea.jsp

Ma'ayan lab

PFAM_InterPro_domains

Proteins that share a structural domain

http://pfam.sanger.ac.uk and http://www.ebi.ac.uk/interpro

Ma'ayan lab

Predcited_microRNAs

Predicted microRNAs that bind to mRNA of sets of genes

http://www.targetscan.org http://microrna.sanger.ac.uk/sequences

Ma'ayan lab

Protein_interaction_hubs

Proteins that interacts with many other proteins

Protein interactions collected from several mammalian protein interactions databases http://actin.pharm.mssm.edu/genes2networks

Ma'ayan lab

  1. Columns include: a) File name as it appears in the drop-down box in the overlap feature on the web-page; b) Description of the content of the gene-list library; c) URL of the source of the data. d) Library created by.