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Items: 1 to 20 of 157

1.

Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph.

Richards AJ, Muller B, Shotwell M, Cowart LA, Rohrer B, Lu X.

Bioinformatics. 2010 Jun 15;26(12):i79-87. doi: 10.1093/bioinformatics/btq203.

2.

Revealing functionally coherent subsets using a spectral clustering and an information integration approach.

Richards AJ, Schwacke JH, Rohrer B, Cowart LA, Lu X.

BMC Syst Biol. 2012;6 Suppl 3:S7. doi: 10.1186/1752-0509-6-S3-S7. Epub 2012 Dec 17.

3.

GRYFUN: a web application for GO term annotation visualization and analysis in protein sets.

Bastos HP, Sousa L, Clarke LA, Couto FM.

PLoS One. 2015 Mar 20;10(3):e0119631. doi: 10.1371/journal.pone.0119631. eCollection 2015.

4.

GS2: an efficiently computable measure of GO-based similarity of gene sets.

Ruths T, Ruths D, Nakhleh L.

Bioinformatics. 2009 May 1;25(9):1178-84. doi: 10.1093/bioinformatics/btp128. Epub 2009 Mar 16.

5.

geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification.

Reboiro-Jato M, Arrais JP, Oliveira JL, Fdez-Riverola F.

BMC Bioinformatics. 2014 Jan 30;15:31. doi: 10.1186/1471-2105-15-31.

6.

GObar: a gene ontology based analysis and visualization tool for gene sets.

Lee JS, Katari G, Sachidanandam R.

BMC Bioinformatics. 2005 Jul 25;6:189.

7.

EnrichNet: network-based gene set enrichment analysis.

Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A.

Bioinformatics. 2012 Sep 15;28(18):i451-i457. doi: 10.1093/bioinformatics/bts389.

8.
9.

GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis.

Powell JA.

BMC Bioinformatics. 2014 May 17;15:146. doi: 10.1186/1471-2105-15-146.

10.

htsint: a Python library for sequencing pipelines that combines data through gene set generation.

Richards AJ, Herrel A, Bonneaud C.

BMC Bioinformatics. 2015 Sep 24;16:307. doi: 10.1186/s12859-015-0729-3.

11.

Mining gene expression data by interpreting principal components.

Roden JC, King BW, Trout D, Mortazavi A, Wold BJ, Hart CE.

BMC Bioinformatics. 2006 Apr 7;7:194.

12.

Combining multiple tools outperforms individual methods in gene set enrichment analyses.

Alhamdoosh M, Ng M, Wilson NJ, Sheridan JM, Huynh H, Wilson MJ, Ritchie ME.

Bioinformatics. 2017 Feb 1;33(3):414-424. doi: 10.1093/bioinformatics/btw623.

13.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

14.

Assessment of protein set coherence using functional annotations.

Chagoyen M, Carazo JM, Pascual-Montano A.

BMC Bioinformatics. 2008 Oct 20;9:444. doi: 10.1186/1471-2105-9-444.

15.

Onto-Tools: new additions and improvements in 2006.

Khatri P, Voichita C, Kattan K, Ansari N, Khatri A, Georgescu C, Tarca AL, Draghici S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W206-11. Epub 2007 Jun 21.

16.

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis.

Yu G, Wang LG, Yan GR, He QY.

Bioinformatics. 2015 Feb 15;31(4):608-9. doi: 10.1093/bioinformatics/btu684. Epub 2014 Oct 17.

PMID:
25677125
17.

FuncBase: a resource for quantitative gene function annotation.

Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP.

Bioinformatics. 2010 Jul 15;26(14):1806-7. doi: 10.1093/bioinformatics/btq265. Epub 2010 May 21.

18.

Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data.

Ma S, Jiang T, Jiang R.

Bioinformatics. 2015 Feb 15;31(4):563-71. doi: 10.1093/bioinformatics/btu672. Epub 2014 Oct 15.

PMID:
25322838
19.

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.

Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma'ayan A.

Bioinformatics. 2015 Sep 15;31(18):3060-2. doi: 10.1093/bioinformatics/btv297. Epub 2015 May 13.

20.

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