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Items: 1 to 20 of 94

1.

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems.

Geistlinger L, Csaba G, Küffner R, Mulder N, Zimmer R.

Bioinformatics. 2011 Jul 1;27(13):i366-73. doi: 10.1093/bioinformatics/btr228.

2.

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.

Merico D, Isserlin R, Stueker O, Emili A, Bader GD.

PLoS One. 2010 Nov 15;5(11):e13984. doi: 10.1371/journal.pone.0013984.

3.

Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets.

Hormoz S, Bhanot G, Biehl M, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Dayarian A.

Bioinformatics. 2015 Feb 15;31(4):492-500. doi: 10.1093/bioinformatics/btu569. Epub 2014 Aug 24.

4.

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.

5.

GAGE: generally applicable gene set enrichment for pathway analysis.

Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ.

BMC Bioinformatics. 2009 May 27;10:161. doi: 10.1186/1471-2105-10-161.

6.

RelExplain-integrating data and networks to explain biological processes.

Berchtold E, Csaba G, Zimmer R.

Bioinformatics. 2017 Jun 15;33(12):1837-1844. doi: 10.1093/bioinformatics/btx060.

PMID:
28165113
7.

Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis.

Geistlinger L, Csaba G, Zimmer R.

BMC Bioinformatics. 2016 Jan 20;17:45. doi: 10.1186/s12859-016-0884-1.

8.

Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis.

Chouvardas P, Kollias G, Nikolaou C.

BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:181. doi: 10.1186/s12859-016-1040-7.

9.

Detecting discordance enrichment among a series of two-sample genome-wide expression data sets.

Lai Y, Zhang F, Nayak TK, Modarres R, Lee NH, McCaffrey TA.

BMC Genomics. 2017 Jan 25;18(Suppl 1):1050. doi: 10.1186/s12864-016-3265-2.

10.

Multi-edge gene set networks reveal novel insights into global relationships between biological themes.

Parikh JR, Xia Y, Marto JA.

PLoS One. 2012;7(9):e45211. doi: 10.1371/journal.pone.0045211. Epub 2012 Sep 13.

11.

Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles.

Edelman E, Porrello A, Guinney J, Balakumaran B, Bild A, Febbo PG, Mukherjee S.

Bioinformatics. 2006 Jul 15;22(14):e108-16.

PMID:
16873460
12.

BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses.

Spinelli L, Carpentier S, Montañana Sanchis F, Dalod M, Vu Manh TP.

BMC Genomics. 2015 Oct 19;16:814. doi: 10.1186/s12864-015-2012-4.

13.

ADAGE signature analysis: differential expression analysis with data-defined gene sets.

Tan J, Huyck M, Hu D, Zelaya RA, Hogan DA, Greene CS.

BMC Bioinformatics. 2017 Nov 22;18(1):512. doi: 10.1186/s12859-017-1905-4.

14.

NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases.

Di Lena P, Martelli PL, Fariselli P, Casadio R.

BMC Genomics. 2015;16 Suppl 8:S6. doi: 10.1186/1471-2164-16-S8-S6. Epub 2015 Jun 18.

15.

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data.

Jupiter D, Chen H, VanBuren V.

BMC Bioinformatics. 2009 Oct 14;10:332. doi: 10.1186/1471-2105-10-332.

16.

Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data.

Berchtold E, Csaba G, Zimmer R.

PLoS One. 2016 Oct 10;11(10):e0164513. doi: 10.1371/journal.pone.0164513. eCollection 2016.

17.

Testing gene set enrichment for subset of genes: Sub-GSE.

Yan X, Sun F.

BMC Bioinformatics. 2008 Sep 2;9:362. doi: 10.1186/1471-2105-9-362.

18.

Inferring pathway crosstalk networks using gene set co-expression signatures.

Wang T, Gu J, Yuan J, Tao R, Li Y, Li S.

Mol Biosyst. 2013 Jul;9(7):1822-8. doi: 10.1039/c3mb25506a. Epub 2013 Apr 17.

PMID:
23591523
19.

Discovering causal signaling pathways through gene-expression patterns.

Parikh JR, Klinger B, Xia Y, Marto JA, Blüthgen N.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W109-17. doi: 10.1093/nar/gkq424. Epub 2010 May 21.

20.

Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data.

Turcan S, Vetter DE, Maron JL, Wei X, Slonim DK.

Pac Symp Biocomput. 2011:50-61.

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