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Items: 1 to 20 of 133

1.

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems.

Kaimal V, Bardes EE, Tabar SC, Jegga AG, Aronow BJ.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W96-102. doi: 10.1093/nar/gkq418. Epub 2010 May 19.

2.

Lists2Networks: integrated analysis of gene/protein lists.

Lachmann A, Ma'ayan A.

BMC Bioinformatics. 2010 Feb 12;11:87. doi: 10.1186/1471-2105-11-87.

3.

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.

4.

CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes.

Jegga AG, Gupta A, Gowrisankar S, Deshmukh MA, Connolly S, Finley K, Aronow BJ.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W408-11. Erratum in: Nucleic Acids Res. 2005;33(13):4377.

5.

Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering.

Aibar S, Fontanillo C, Droste C, De Las Rivas J.

Bioinformatics. 2015 May 15;31(10):1686-8. doi: 10.1093/bioinformatics/btu864. Epub 2015 Jan 18.

6.

Inferring the regulatory network behind a gene expression experiment.

Bleda M, Medina I, Alonso R, De Maria A, Salavert F, Dopazo J.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W168-72. doi: 10.1093/nar/gks573. Epub 2012 Jun 11.

7.

DEFOG: discrete enrichment of functionally organized genes.

Wittkop T, Berman AE, Fleisch KM, Mooney SD.

Integr Biol (Camb). 2012 Jul;4(7):795-804. doi: 10.1039/c2ib00136e. Epub 2012 Jun 18.

8.

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information.

Nogales-Cadenas R, Carmona-Saez P, Vazquez M, Vicente C, Yang X, Tirado F, Carazo JM, Pascual-Montano A.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W317-22. doi: 10.1093/nar/gkp416. Epub 2009 May 22.

9.

CRSD: a comprehensive web server for composite regulatory signature discovery.

Liu CC, Lin CC, Chen WS, Chen HY, Chang PC, Chen JJ, Yang PC.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W571-7.

10.

DiRE: identifying distant regulatory elements of co-expressed genes.

Gotea V, Ovcharenko I.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W133-9. doi: 10.1093/nar/gkn300. Epub 2008 May 17.

11.

GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.

Feng C, Araki M, Kunimoto R, Tamon A, Makiguchi H, Niijima S, Tsujimoto G, Okuno Y.

BMC Genomics. 2009 Sep 3;10:411. doi: 10.1186/1471-2164-10-411.

12.

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data.

Guan D, Shao J, Zhao Z, Wang P, Qin J, Deng Y, Boheler KR, Wang J, Yan B.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W130-6. doi: 10.1093/nar/gku471. Epub 2014 May 29.

13.

From promoter analysis to transcriptional regulatory network prediction using PAINT.

Gonye GE, Chakravarthula P, Schwaber JS, Vadigepalli R.

Methods Mol Biol. 2007;408:49-68. doi: 10.1007/978-1-59745-547-3_4.

PMID:
18314577
14.

ASIAN: a web server for inferring a regulatory network framework from gene expression profiles.

Aburatani S, Goto K, Saito S, Toh H, Horimoto K.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W659-64.

15.

GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space.

Zhong S, Storch KF, Lipan O, Kao MC, Weitz CJ, Wong WH.

Appl Bioinformatics. 2004;3(4):261-4.

PMID:
15702958
16.

Prioritizing genes for pathway impact using network analysis.

Chang AN.

Methods Mol Biol. 2009;563:141-56. doi: 10.1007/978-1-60761-175-2_8.

PMID:
19597784
17.
18.

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).

Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN.

BMC Bioinformatics. 2005 Jul 5;6:168.

19.

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions.

De Preter K, Barriot R, Speleman F, Vandesompele J, Moreau Y.

Nucleic Acids Res. 2008 Apr;36(7):e43. doi: 10.1093/nar/gkn114. Epub 2008 Mar 16.

20.

mirAct: a web tool for evaluating microRNA activity based on gene expression data.

Liang Z, Zhou H, He Z, Zheng H, Wu J.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W139-44. doi: 10.1093/nar/gkr351. Epub 2011 May 19.

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