FunRich pipeline

FunRich specifications

Information


Unique identifier OMICS_15301
Name FunRich
Alternative name FUNctionnal enRICHment analysis tool
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Version 3.0
Stability Stable
Requirements Net framework
Maintained Yes

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Maintainer


  • person_outline Suresh Mathivanan <>

Publication for FUNctionnal enRICHment analysis tool

FunRich IN pipelines

 (5)
2018
PMCID: 5820528
PMID: 29503661
DOI: 10.3389/fgene.2018.00042

[…] of apoptosis (go:0042981, 11 degs), and cell morphogenesis (go:0000902, 10 degs). to further explore the biological process of the shared degs, a separate enrichment analysis using stand-alone funrich v3 software was completed. as a result, signal transduction (42.2% degs), cell communication (39.5% degs), cell growth and/or maintenance (13.6% degs), apoptosis (3.3% degs) and regulation […]

2017
PMCID: 5311114
PMID: 28217743
DOI: 10.1128/mSphere.00038-17

[…] using the tuxedo suite of tools (74). a summary of the results of the expression analysis is available in data set s1 in the supplemental material. gene ontology analysis was performed using funrich (75). analysis and visualization of metabolic networks utilized cytoscape (76)., this study is based upon work supported by the u.s. department of energy (doe), office of science, office […]

2017
PMCID: 5345195
PMID: 28283027
DOI: 10.1186/s40478-017-0421-0

[…] determine whether modules corresponded to particular subcellular components, we mined the subcellular organelle database organelledb [105]. we also assed the exosomal content of each module with the funrich tool [81], exploiting the extracellular vesicles database [52]. next, we performed gene ontology and pathway analysis using a web based tool, enrichr [56], as well as cluego and cluepedia […]

2017
PMCID: 5575162
PMID: 28852045
DOI: 10.1038/s41598-017-10127-1

[…] enrichment analysis. simply, the identified cem, degs-et, degs-ot and tepgs were then used to obtain functional pathways and go term. relevant go terms for those gene set were analyzed by using funrich software (http://www.funrich.org)19. enriched pathways and drugs were identified by using toppcluster (https://toppcluster.cchmc.org/)20. the functional annotations for the go term level […]

2017
PMCID: 5575162
PMID: 28852045
DOI: 10.1038/s41598-017-10127-1

[…] the identified cem, degs-et, degs-ot and tepgs were then used to obtain functional pathways and go term. relevant go terms for those gene set were analyzed by using funrich software (http://www.funrich.org)19. enriched pathways and drugs were identified by using toppcluster (https://toppcluster.cchmc.org/)20. the functional annotations for the go term level were mainly focused on biological […]

FunRich institution(s)
Department of Electronic Engineering, La Trobe University, Bundoora, Australia; 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; 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; 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; Department of Surgery (RMH), University of Melbourne, Parkville, Australia; ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Parkville, Australia; Department of Biochemistry and Molecular Biology, Monash University, Australia
FunRich funding source(s)
This work was funded by the Australian NH&MRC fellowship (1016599), the Australian Research Council Discovery project (DP130100535) and the Australian Research Council DECRA (DE150101777, 381413).

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