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GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.

Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, Quackenbush J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1060-6. doi: 10.1093/nar/gkr901. Epub 2011 Nov 21.


GeneSigDB--a curated database of gene expression signatures.

Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush J.

Nucleic Acids Res. 2010 Jan;38(Database issue):D716-25. doi: 10.1093/nar/gkp1015. Epub 2009 Nov 24.


The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons.

Ho Sui SJ, Begley K, Reilly D, Chapman B, McGovern R, Rocca-Sera P, Maguire E, Altschuler GM, Hansen TA, Sompallae R, Krivtsov A, Shivdasani RA, Armstrong SA, Culhane AC, Correll M, Sansone SA, Hofmann O, Hide W.

Nucleic Acids Res. 2012 Jan;40(Database issue):D984-91. doi: 10.1093/nar/gkr1051. Epub 2011 Nov 24.


Systems biology approach to identify gene network signatures for colorectal cancer.

Sonachalam M, Shen J, Huang H, Wu X.

Front Genet. 2012 May 17;3:80. doi: 10.3389/fgene.2012.00080. eCollection 2012.


Liverome: a curated database of liver cancer-related gene signatures with self-contained context information.

Lee L, Wang K, Li G, Xie Z, Wang Y, Xu J, Sun S, Pocalyko D, Bhak J, Kim C, Lee KH, Jang YJ, Yeom YI, Yoo HS, Hwang S.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S3. doi: 10.1186/1471-2164-12-S3-S3. Epub 2011 Nov 30.


PGDB: a curated and integrated database of genes related to the prostate.

Li LC, Zhao H, Shiina H, Kane CJ, Dahiya R.

Nucleic Acids Res. 2003 Jan 1;31(1):291-3.


Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database.

Cheng WC, Tsai ML, Chang CW, Huang CL, Chen CR, Shu WY, Lee YS, Wang TH, Hong JH, Li CY, Hsu IC.

BMC Bioinformatics. 2010 Aug 10;11:421. doi: 10.1186/1471-2105-11-421.


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.


SIGNATURE: a workbench for gene expression signature analysis.

Chang JT, Gatza ML, Lucas JE, Barry WT, Vaughn P, Nevins JR.

BMC Bioinformatics. 2011 Nov 14;12:443. doi: 10.1186/1471-2105-12-443.


Quantitative comparison of microarray experiments with published leukemia related gene expression signatures.

Klein HU, Ruckert C, Kohlmann A, Bullinger L, Thiede C, Haferlach T, Dugas M.

BMC Bioinformatics. 2009 Dec 15;10:422. doi: 10.1186/1471-2105-10-422.


TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

Lopez F, Textoris J, Bergon A, Didier G, Remy E, Granjeaud S, Imbert J, Nguyen C, Puthier D.

PLoS One. 2008;3(12):e4001. doi: 10.1371/journal.pone.0004001. Epub 2008 Dec 23.


DDEC: Dragon database of genes implicated in esophageal cancer.

Essack M, Radovanovic A, Schaefer U, Schmeier S, Seshadri SV, Christoffels A, Kaur M, Bajic VB.

BMC Cancer. 2009 Jul 6;9:219. doi: 10.1186/1471-2407-9-219.


The resource: targets and expression.

Betel D, Wilson M, Gabow A, Marks DS, Sander C.

Nucleic Acids Res. 2008 Jan;36(Database issue):D149-53. Epub 2007 Dec 23.


MGEx-Udb: a mammalian uterus database for expression-based cataloguing of genes across conditions, including endometriosis and cervical cancer.

Bajpai AK, Davuluri S, Chandrashekar DS, Ilakya S, Dinakaran M, Acharya KK.

PLoS One. 2012;7(5):e36776. doi: 10.1371/journal.pone.0036776. Epub 2012 May 11.


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.


DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions.

Yu J, Pacifico S, Liu G, Finley RL Jr.

BMC Genomics. 2008 Oct 7;9:461. doi: 10.1186/1471-2164-9-461.


Importing MAGE-ML format microarray data into BioConductor.

Durinck S, Allemeersch J, Carey VJ, Moreau Y, De Moor B.

Bioinformatics. 2004 Dec 12;20(18):3641-2. Epub 2004 Jul 15.


TreeFam: a curated database of phylogenetic trees of animal gene families.

Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80.


Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME.

Finocchiaro G, Mancuso FM, Cittaro D, Muller H.

Nucleic Acids Res. 2007;35(7):2343-55. Epub 2007 Mar 27.


PRGdb: a bioinformatics platform for plant resistance gene analysis.

Sanseverino W, Roma G, De Simone M, Faino L, Melito S, Stupka E, Frusciante L, Ercolano MR.

Nucleic Acids Res. 2010 Jan;38(Database issue):D814-21. doi: 10.1093/nar/gkp978. Epub 2009 Nov 11.

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