Gene Lists Pathway Analysis (Public)
- TSEA Tissue Specific expression using GTEx http://genetics.wustl.edu/jdlab/tsea/
- Enrichr http://amp.pharm.mssm.edu/Enrichr/
- Dena comment: performed cell type enrichment successfully
CTen is an enrichment algorithm to identify changes in the cell-type demographics of in vivo tissue samples.
- Metascape http://metascape.org/gp/index.html#/main/step1 good also for mutiple lists
- String - database of protein interactions (~2000 organisms) http://string-db.org/cgi/about.pl?UserId=9CZxsyKvk8G8&sessionId=0cBqU3p3zdbc
- g:Profiler - a tool for functional profiling https://biit.cs.ut.ee/gprofiler/gost accepts multiple lists, custom background, supports many species and databases
Table of tools for functional analysis
| Tool | URL | Species | Custom reference | Databases | Integration of databases | Format results | Last Update | Easy to use(1- difficult … 5 - easy) | Easy to download results (1- difficult … 5 - easy) |
| DAVID | https://david.ncifcrf.gov/ | Thousands | yes | GO, pathways, domains, diseases, interactions, literature and more | yes | tables, heat maps and pathways | 2010 | 5 | 4 |
| WebGestalt | http://bioinfo.vanderbilt.edu/webgestalt/ | human, mouse, rat, worm, fly, yeast, dog, and zebrafish | yes | GO, pathways, motif gene sets, diseases, interactions, genomic location and more | no | tables and dag for GO | 2013 | 5 | 5 |
| Ontologizer | https://charite.github.io/software-ontologizer.html | Custom, any specie if you have annotations | yes | GO | no | custom GO graphs | 2016 | 2 | 3 |
| Enrichr | http://amp.pharm.mssm.edu/Enrichr/ | human and mouse | no | transcription (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 more | no | tables, bar charts,grid, network and clustergram | 2014-15 | 5 | 5 |
| ThaleMine* | https://apps.araport.org/thalemine/begin.do | Arabidopsis* | no | GO, pathways, genomic location, protein domains and publication enrichment | no | tables | 2016 | 5 | 4 |
| Reactome | http://www.reactome.org/ | human, mouse, rat, worm, fly, yeast, dog, and zebrafish (10 species, not good for plants) | no | Pathways defined by the reactome team | no | tables and pathways diagrams | 2016 | 4 | 4 |
| GSEA | http://software.broadinstitute.org/gsea/index.jsp | human, mouse | not relevant | molecular signature databases (http://software.broadinstitute.org/gsea/msigdb/index.jsp): hallmarks, GO, pathways, motif gene sets, oncogenic and immunological signatures, genomic location and more | yes | tables and enrichment scores per term | 2016 | 3 | 5 |
| Ingenuity | http://www.ingenuity.com/products/ipa *needs a license | human, mouse rat, Arabidopsis, Bos taurus, worm, dog, zebrafish, fruit fly, chicken, Rhesus Monkey, chimpanzee, yeast (good for mammals) | yes | Entrez 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 TargetScan miRecords Clinicaltrials.gov 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) | yes | tables, bar charts, heatmap, pathways diagrams and networks | 2016 (every quarter) | 4 | 5 |
| Visualization Tools | |||||||||
| Revigo | http://revigo.irb.hr/ | 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 clouds | 2014, less relevant | 4 | 3 | |||
| Cytoscape | www.cytoscape.org/ | 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 formats | not relevant | 1 | 4 | |||
| * Part of InterMine | http://intermine.org/ | FlyMine - 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 | |||||||||
| FlyTF.org - Drosophila transcription factors | |||||||||
| MitoMiner - proteomic data for mitochondria | |||||||||
| HumanMine - human | |||||||||
| PhytoMine - plants | |||||||||
| MedicMine - Medicago truncatula | |||||||||