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Bioinformatics and Statistics Resources: Software (Pathway/Enrichment)

Information and resources on bioinformatics and statistics for the UCSF research community

Pathway/Enrichment Analysis

The resources below are all free. Many other pathway/enrichment and network analysis software programs such as Ingenuity Pathway Analysis (IPA) are available at cost to individual labs and researchers (UCSF no longer maintains an institutional agreement with IPA). If you find additional free resources that you think should be listed here, please email Karla Lindquist. The content on this page has been contributed to with help from UCSF colleagues (special thanks to Dr. Saúl Lira Albarrán). I am very grateful for any assistance in keeping this list of free resources up to date.



"ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network."

ClueGO is freely available to download.



"This tool suite, introduced in the first version of DAVID, mainly provides typical batch annotation and gene-GO term enrichment analysis to highlight the most relevant GO terms associated with a given gene list."

DAVID is freely available as a web-based resource.



Enrichr is "an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results...". (Chen et al. BMC Bioinformatics 2013)

Enrichr is freely available as a web-based resource.



"FunRich is a stand-alone software tool used mainly for functional enrichment and interaction network analysis of genes and proteins. Besides, the results of the analysis can be depicted graphically in the form of Venn, Bar, Column, Pie and Doughnut charts."

FunRich is freely available for download.

g.Profiler g:GOSt


"g:GOSt performs functional enrichment analysis, also known as over-representation analysis (ORA) or gene set enrichment analysis, on input gene list. It maps genes to known functional information sources and detects statistically significantly enriched terms."

g:GOSt is freely available as a web-based resource.



"GO-Elite is an application designed to identify a non-redundant set of ontology (e.g., Gene Ontology) terms, gene sets (e.g., transcription factor targets) and pathways (e.g., WikiPathways) to describe a particular set of genes or metabolites."

GO-Elite is freely available for download or as a web-based resource.



"Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes)."

GSEA is freely available for download or as a web-based resource.



"Next-gen pathway analysis using Advaita’s proprietary “Impact Analysis” method to identify significant pathways without all the noise found in other approaches. iPathwayGuide provides publication-ready results in minutes."

iPathwayGuide is freely available as a web-based resource.



"The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis."

PANTHER is freely available as a web-based resource.



"A factor graph framework for pathway inference on high-throughput genomic data."

PARADIGM is freely available for download.


"PathVisio is a free open-source pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. It is developed in Java and can be extended with plugins."

PathVisio is freely available for download.

Pathway Commons

"Access and discover data integrated from public pathway and interactions databases."

Pathway Commons is freely available as a web-based resource.

R Bioconductor



Bioconductor has quite a few packages designed for pathway and enrichment analysis, such as SPIA, pathview, clipper, gage, graphite, Pathnet, and others. R programming experience is required.

R and Bioconductor are freely available for download.




"Reactome is a free, open-source, curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education."

Reactome is freely available as a web-based resource.



"WebGestalt (WEB-based Gene SeT AnaLysis Toolkit) is a functional enrichment analysis web tool".

WebGestalt is freely available as a web-based resource.