FunRich: An open access standalone functional enrichment and interaction network analysis tool

Mohashin Pathan; Shivakumar Keerthikumar; Ching-Seng Ang; Lahiru Gangoda; Camelia Y J Quek; Nicholas A Williamson; Dmitri Mouradov; Oliver M Sieber; Richard J Simpson; Agus Salim; Antony Bacic; Andrew F Hill; David A Stroud; Michael T Ryan; Johnson I Agbinya; John M Mariadason; Antony W Burgess; Suresh Mathivanan

doi:10.1002/pmic.201400515

FunRich: An open access standalone functional enrichment and interaction network analysis tool

Proteomics. 2015 Aug;15(15):2597-601. doi: 10.1002/pmic.201400515. Epub 2015 Jun 17.

Authors

Mohashin Pathan¹, Shivakumar Keerthikumar², Ching-Seng Ang³, Lahiru Gangoda², Camelia Y J Quek^{3

4}, Nicholas A Williamson³, Dmitri Mouradov⁵, Oliver M Sieber^{5

6}, Richard J Simpson², Agus Salim⁷, Antony Bacic^{3

8}, Andrew F Hill^{2

3

4}, David A Stroud⁹, Michael T Ryan⁹, Johnson I Agbinya¹, John M Mariadason¹⁰, Antony W Burgess^{5

11}, Suresh Mathivanan²

Affiliations

¹ Department of Electronic Engineering, La Trobe University, Bundoora, Australia.
² Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
³ The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.
⁴ Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia.
⁵ Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
⁶ Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville, Australia.
⁷ Department of Mathematics and Statistics, La Trobe University, Bundoora, Australia.
⁸ ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Parkville, VIC 3010, Australia.
⁹ Department of Biochemistry and Molecular Biology, Monash University, Australia.
¹⁰ Olivia Newton John Cancer Research Institute, Melbourne, Australia, Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Australia, School of Cancer Medicine, La Trobe University, Melbourne, Australia.
¹¹ Department of Surgery (RMH), University of Melbourne, Parkville, Australia.

PMID: 25921073
DOI: 10.1002/pmic.201400515

Abstract

As high-throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user-friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed to be used by biologists with minimal or no support from computational and database experts. Using FunRich, users can perform functional enrichment analysis on background databases that are integrated from heterogeneous genomic and proteomic resources (>1.5 million annotations). Besides default human specific FunRich database, users can download data from the UniProt database, which currently supports 20 different taxonomies against which enrichment analysis can be performed. Moreover, the users can build their own custom databases and perform the enrichment analysis irrespective of organism. In addition to proteomics datasets, the custom database allows for the tool to be used for genomics, lipidomics and metabolomics datasets. Thus, FunRich allows for complete database customization and thereby permits for the tool to be exploited as a skeleton for enrichment analysis irrespective of the data type or organism used. FunRich (http://www.funrich.org) is user-friendly and provides graphical representation (Venn, pie charts, bar graphs, column, heatmap and doughnuts) of the data with customizable font, scale and color (publication quality).

Keywords: Bioinformatics; Enrichment analysis; Interaction networks; Omics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Data Interpretation, Statistical
Gene Expression Profiling / methods
Gene Ontology
Gene Regulatory Networks*
Genomics / methods
Humans
Internet
Metabolomics / methods
Protein Interaction Maps*
Proteomics / methods
Reproducibility of Results
Software*
User-Computer Interface