Next generation software for functional trend analysis - PubMed (original) (raw)
Next generation software for functional trend analysis
Gabriel F Berriz et al. Bioinformatics. 2009.
Abstract
FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with a new interface and several new features. For example, enrichment analysis can now be performed within multiple gene- and protein-naming systems. This feature avoids potentially serious translation artifacts to which other enrichment analysis strategies are subject.
Availability: The FuncAssociate web application is freely available to all users at http://llama.med.harvard.edu/funcassociate.
Similar articles
- Characterizing gene sets with FuncAssociate.
Berriz GF, King OD, Bryant B, Sander C, Roth FP. Berriz GF, et al. Bioinformatics. 2003 Dec 12;19(18):2502-4. doi: 10.1093/bioinformatics/btg363. Bioinformatics. 2003. PMID: 14668247 - The Synergizer service for translating gene, protein and other biological identifiers.
Berriz GF, Roth FP. Berriz GF, et al. Bioinformatics. 2008 Oct 1;24(19):2272-3. doi: 10.1093/bioinformatics/btn424. Epub 2008 Aug 12. Bioinformatics. 2008. PMID: 18697767 Free PMC article. - Saint: a lightweight integration environment for model annotation.
Lister AL, Pocock M, Taschuk M, Wipat A. Lister AL, et al. Bioinformatics. 2009 Nov 15;25(22):3026-7. doi: 10.1093/bioinformatics/btp523. Epub 2009 Sep 4. Bioinformatics. 2009. PMID: 19734151 Free PMC article. - Using MetaboAnalyst 4.0 for Metabolomics Data Analysis, Interpretation, and Integration with Other Omics Data.
Chong J, Xia J. Chong J, et al. Methods Mol Biol. 2020;2104:337-360. doi: 10.1007/978-1-0716-0239-3_17. Methods Mol Biol. 2020. PMID: 31953825 Review. - The Bioverse API and web application.
Guerquin M, McDermott J, Frazier Z, Samudrala R. Guerquin M, et al. Methods Mol Biol. 2009;541:511-34. doi: 10.1007/978-1-59745-243-4_22. Methods Mol Biol. 2009. PMID: 19381533 Review.
Cited by
- Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.
Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML. Gordân R, et al. Genome Biol. 2011 Dec 21;12(12):R125. doi: 10.1186/gb-2011-12-12-r125. Genome Biol. 2011. PMID: 22189060 Free PMC article. - Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila.
Busser BW, Haimovich J, Huang D, Ovcharenko I, Michelson AM. Busser BW, et al. Nucleic Acids Res. 2015 Feb 18;43(3):1726-39. doi: 10.1093/nar/gkv011. Epub 2015 Jan 21. Nucleic Acids Res. 2015. PMID: 25609699 Free PMC article. - Mapping the Hsp90 genetic interaction network in Candida albicans reveals environmental contingency and rewired circuitry.
Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE. Diezmann S, et al. PLoS Genet. 2012;8(3):e1002562. doi: 10.1371/journal.pgen.1002562. Epub 2012 Mar 15. PLoS Genet. 2012. PMID: 22438817 Free PMC article. - In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan.
Jorba G, Aguirre-Plans J, Junet V, Segú-Vergés C, Ruiz JL, Pujol A, Fernández-Fuentes N, Mas JM, Oliva B. Jorba G, et al. PLoS One. 2020 Feb 13;15(2):e0228926. doi: 10.1371/journal.pone.0228926. eCollection 2020. PLoS One. 2020. PMID: 32053711 Free PMC article. - A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells.
Tian AL, Lu M, Calderón-Mantilla G, Petsalaki E, Dottorini T, Tian X, Wang Y, Huang SY, Hou JL, Li X, Elsheikha HM, Zhu XQ. Tian AL, et al. Parasit Vectors. 2018 Mar 6;11(1):152. doi: 10.1186/s13071-018-2745-4. Parasit Vectors. 2018. PMID: 29510740 Free PMC article.
References
- Berriz GF, et al. Characterizing gene sets with Func Associate. Bioinformatics. 2003;19:2502–2504. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
- NS054052/NS/NINDS NIH HHS/United States
- NS035611/NS/NINDS NIH HHS/United States
- HG003224/HG/NHGRI NIH HHS/United States
- U01 HL081341/HL/NHLBI NIH HHS/United States
- HG0017115/HG/NHGRI NIH HHS/United States
- P01 NS035611/NS/NINDS NIH HHS/United States
- R01 HG003224/HG/NHGRI NIH HHS/United States
- HL081341/HL/NHLBI NIH HHS/United States
- P50 HG004233/HG/NHGRI NIH HHS/United States
- R01 NS054052/NS/NINDS NIH HHS/United States
- HG004233/HG/NHGRI NIH HHS/United States
LinkOut - more resources
Full Text Sources
Other Literature Sources