FunRich: An open access standalone functional enrichment and interaction network analysis tool.
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).
Department of Electronic Engineering, La Trobe University, Bundoora, Australia.
Mohashin
M
Pathan
Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
Shivakumar
S
Keerthikumar
The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.
Ching-Seng
CS
Ang
Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
Lahiru
L
Gangoda
The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.|Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia.
Camelia Y J
CY
Quek
The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.
Nicholas A
NA
Williamson
Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.
Dmitri
D
Mouradov
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.
Oliver M
OM
Sieber
Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
Richard J
RJ
Simpson
Department of Mathematics and Statistics, La Trobe University, Bundoora, Australia.
Agus
A
Salim
The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.|ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Parkville, VIC 3010, Australia.
Antony
A
Bacic
Department of Biochemistry, La Trobe Institute for Molecular Science, 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.
Andrew F
AF
Hill
Department of Biochemistry and Molecular Biology, Monash University, Australia.
David A
DA
Stroud
Department of Biochemistry and Molecular Biology, Monash University, Australia.
Michael T
MT
Ryan
Department of Electronic Engineering, La Trobe University, Bundoora, Australia.
Johnson I
JI
Agbinya
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.
John M
JM
Mariadason
Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.|Department of Surgery (RMH), University of Melbourne, Parkville, Australia.
Antony W
AW
Burgess
Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
Suresh
S
Mathivanan
D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D055432:Metabolomics / Q000379:methods; D060066:Protein Interaction Maps; D040901:Proteomics / Q000379:methods; D015203:Reproducibility of Results; D012984:Software; D014584:User-Computer Interface
Bioinformatics; Enrichment analysis; Interaction networks; Omics