Table 1

GMT files used for gene-list overlap analysis in L2N

Name

Description

Source

GMT File Creator

WikiPathways_pathways

Biological pathways

http://www.wikipathways.org webcite

Ma'ayan lab

Reactome_pathways

Biological pathways

http://www.reactome.org webcite

Ma'ayan lab

GenMAPP_patwhays

Biological pathways

http://www.genmapp.org webcite

MSigDB

KEGG_pathways

Signaling pathways

http://www.genome.jp/kegg webcite

MSigDB

BioCarta_pathways

Signaling pathways

http://www.biocarta.com webcite

MSigDB

Chromosome_location

Chromosome location

http://genome.ucsc.edu webcite

MSigDB

TFs_predicted_binidng_sites

TRANSFAC predicted sites

http://genome.ucsc.edu webcite

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 webcite

Ma'ayan lab

Gene_Ontology_MF

Gene Ontology Molecular Function

http://www.geneontology.org webcite

Ma'ayan lab

Gene_Ontology_CC

Gene Ontology Cellular Component

http://www.geneontology.org webcite

Ma'ayan lab

HMDB_metabolites

Genes associated with Metabolites

http://www.hmdb.ca webcite

Ma'ayan lab

OMIM_disease_genes

Genes associated with a specific disease

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

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 webcite and http://actin.pharm.mssm.edu/genes2networks webcite

Ma'ayan lab

KEA_kinases

Substrates of protein kinases collected from different databases

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

Ma'ayan lab

PFAM_InterPro_domains

Proteins that share a structural domain

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

Ma'ayan lab

Predcited_microRNAs

Predicted microRNAs that bind to mRNA of sets of genes

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

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 webcite

Ma'ayan lab

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.

Lachmann and Ma'ayan BMC Bioinformatics 2010 11:87   doi:10.1186/1471-2105-11-87