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Items: 1 to 20 of 125

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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.

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.

4.

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.

5.

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.

6.

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.

7.

Gene expression analysis in clear cell renal cell carcinoma using gene set enrichment analysis for biostatistical management.

Maruschke M, Reuter D, Koczan D, Hakenberg OW, Thiesen HJ.

BJU Int. 2011 Jul;108(2 Pt 2):E29-35. doi: 10.1111/j.1464-410X.2010.09794.x. Epub 2011 Mar 16.

8.

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.

9.

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.

10.

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.

11.

Comparative study of gene set enrichment methods.

Abatangelo L, Maglietta R, Distaso A, D'Addabbo A, Creanza TM, Mukherjee S, Ancona N.

BMC Bioinformatics. 2009 Sep 2;10:275. doi: 10.1186/1471-2105-10-275.

12.

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.

13.

Gene co-expression network topology provides a framework for molecular characterization of cellular state.

Carter SL, Brechbühler CM, Griffin M, Bond AT.

Bioinformatics. 2004 Sep 22;20(14):2242-50. Epub 2004 May 6.

14.

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
15.

A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.

Keller A, Backes C, Gerasch A, Kaufmann M, Kohlbacher O, Meese E, Lenhof HP.

Bioinformatics. 2009 Nov 1;25(21):2787-94. doi: 10.1093/bioinformatics/btp510. Epub 2009 Aug 27.

16.

Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana.

Schuler M, Keller A, Backes C, Philippar K, Lenhof HP, Bauer P.

BMC Plant Biol. 2011 May 18;11:87. doi: 10.1186/1471-2229-11-87.

17.

DEEP--a tool for differential expression effector prediction.

Degenhardt J, Haubrock M, Dönitz J, Wingender E, Crass T.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W619-24. Epub 2007 Jun 21.

18.

Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles.

Prieto C, Risueño A, Fontanillo C, De las Rivas J.

PLoS One. 2008;3(12):e3911. doi: 10.1371/journal.pone.0003911. Epub 2008 Dec 15.

19.

ADGO: analysis of differentially expressed gene sets using composite GO annotation.

Nam D, Kim SB, Kim SK, Yang S, Kim SY, Chu IS.

Bioinformatics. 2006 Sep 15;22(18):2249-53. Epub 2006 Jul 12.

20.

YGA: identifying distinct biological features between yeast gene sets.

Chang DT, Li WS, Bai YH, Wu WS.

Gene. 2013 Apr 10;518(1):26-34. doi: 10.1016/j.gene.2012.11.089. Epub 2012 Dec 22.

PMID:
23266802
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