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Title: FunRich: An open access standalone functional enrichment and interaction network analysis tool.
Austin Authors: Pathan, Mohashin;Keerthikumar, Shivakumar;Ang, Ching-Seng;Gangoda, Lahiru;Quek, Camelia Y J;Williamson, Nicholas A;Mouradov, Dmitri;Sieber, Oliver M;Simpson, Richard J;Salim, Agus;Bacic, Antony;Hill, Andrew F;Stroud, David A;Ryan, Michael T;Agbinya, Johnson I;Mariadason, John M ;Burgess, Antony W;Mathivanan, Suresh
Affiliation: Department of Surgery (RMH), University of Melbourne, Parkville, Australia
Ludwig Institute for Cancer Research, Austin Health, Heidelberg, Victoria, Australia
Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
Department of Electronic Engineering, La Trobe University, Bundoora, Australia
School of Cancer Medicine, La Trobe University, Melbourne, Australia
The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
Faculty of Medicine, Dentistry and Health Sciences, Department of Medical Biology, University of Melbourne, Parkville, Australia
Department of Mathematics and Statistics, La Trobe University, Bundoora, Australia
ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Parkville, VIC 3010, Australia
Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
Department of Biochemistry and Molecular Biology, Monash University, Australia
Issue Date: Aug-2015
Date: 2015-06-17
Publication information: Proteomics 2015; 15(15): 2597-2601
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 ( 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).
DOI: 10.1002/pmic.201400515
Journal: Proteomics
PubMed URL: 25921073
Type: Journal Article
Subjects: Bioinformatics
Enrichment analysis
Interaction networks
Appears in Collections:Journal articles

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