Gene Lists Pathway Analysis (Public)

   CTen is an enrichment algorithm to identify changes in the cell-type demographics of in vivo tissue samples.

Table of tools for functional analysis


ToolURLSpeciesCustom referenceDatabasesIntegration of databasesFormat resultsLast UpdateEasy to use(1- difficult … 5 - easy)Easy to download results (1- difficult … 5 - easy)
DAVID,  pathways, domains, diseases, interactions, literature and moreyestables, heat maps and pathways201054
WebGestalt, mouse, rat, worm, fly, yeast, dog, and zebrafishyesGO, pathways, motif gene sets, diseases, interactions, genomic location and morenotables and dag for GO201355
Ontologizer, any specie if you have annotationsyesGOnocustom GO graphs201623
Enrichr and mousenotranscription (ENCODE_TF  and histome modifications, Epigenomics_Roadmap_HM_ChIP-seq, ChEA, transcription factors, Targetscan),GO, GTEx_Tissue_Sample_Gene_Expression_Profiles, pathways, GeneSigDB, perturbations from GEO, Cancer_Cell_Line_Encyclopedia and morenotables, bar charts,grid, network and clustergram2014-1555
ThaleMine**noGO, pathways, genomic location, protein domains and publication enrichmentnotables201654
Reactome, mouse, rat, worm, fly, yeast, dog, and zebrafish (10 species, not good for plants)noPathways defined by the reactome teamnotables and pathways diagrams201644
GSEA, mousenot relevantmolecular signature databases ( hallmarks, GO,  pathways, motif gene sets, oncogenic and immunological signatures, genomic location and moreyestables and enrichment scores per term201635
Ingenuity                 *needs a licensehuman, mouse rat, Arabidopsis, Bos taurus, worm, dog, zebrafish, fruit fly, chicken, Rhesus Monkey, chimpanzee, yeast
(good for mammals)
yesEntrez Gene  RefSeq
OMIM  GWAS Database  Gene Ontology  Human Metabolome Database (HMDB)  GNF Tissue Expression Body Atlas  NCI-60 Cell Line Expression Atlas KEGG metabolic pathway information  LIGAND enzyme/substrate reactions  BIND, DIP, MINT, MIPS, BIOGRID, INTACT, COGNIA protein-protein interactions TarBase
miRecords  Drugs@FDA  Mosby’s Drug Consult  Goodman & Gilman’s Pharmacological Basis of Therapeutics  DrugBank Hazardous Substance Database (HSDB) Chemical Carcinogenesis Research Information System database (CCRIS)
yestables, bar charts, heatmap, pathways diagrams and networks2016 (every quarter)45

Visualization Tools


REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. 
The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds2014, less relevant43

Visualizing complex networks and integrating these with any type of attribute data, with annotations, gene expression profiles and other state data. Additional features are available as Apps. 
A huge amount of beatiful network graphics in different formatsnot relevant14

* Part of InterMine - Drosophila genomics

modMine - fly and worm modENCODE data

MouseMine - at MGI

RatMine - at RGD

G2CMine - The Genes to Cognition Programme

WormMine - at WormBase

YeastMine - at SGD

ZebrafishMine - at ZFIN

INDIGOmine - microbes

toxoMine - Toxoplasma gondii

ThaleMine - Araport Project with data for Arabidopsis thaliana

TargetMine - drug target discovery - Drosophila transcription factors

MitoMiner - proteomic data for mitochondria

HumanMine - human

PhytoMine - plants

MedicMine - Medicago truncatula