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Items: 1 to 20 of 67

1.

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome.

Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L.

Database (Oxford). 2013 Apr 2;2013:bat013. doi: 10.1093/database/bat013. Print 2013.

2.

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Kuhn A, Luthi-Carter R, Delorenzi M.

BMC Bioinformatics. 2008 Jan 17;9:26. doi: 10.1186/1471-2105-9-26.

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.

4.

MageComet--web application for harmonizing existing large-scale experiment descriptions.

Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.

Bioinformatics. 2012 May 15;28(10):1402-3. doi: 10.1093/bioinformatics/bts148. Epub 2012 Apr 2.

5.

Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array.

Vathipadiekal V, Wang V, Wei W, Waldron L, Drapkin R, Gillette M, Skates S, Birrer M.

Clin Cancer Res. 2015 Nov 1;21(21):4960-9. doi: 10.1158/1078-0432.CCR-14-3173. Epub 2015 May 5.

6.

Integrated analysis of gene expression profile and genetic variations associated with ovarian cancer.

Ge L, Shao GR, Wang HJ, Song SL, Xin G, Wu M, Zhang FX.

Eur Rev Med Pharmacol Sci. 2015;19(14):2703-10.

7.

NetPathMiner: R/Bioconductor package for network path mining through gene expression.

Mohamed A, Hancock T, Nguyen CH, Mamitsuka H.

Bioinformatics. 2014 Nov 1;30(21):3139-41. doi: 10.1093/bioinformatics/btu501. Epub 2014 Jul 28.

8.

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

BMC Bioinformatics. 2007 Apr 19;8:129.

9.

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.

10.

Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns.

Baron D, Dubois E, Bihouée A, Teusan R, Steenman M, Jourdon P, Magot A, Péréon Y, Veitia R, Savagner F, Ramstein G, Houlgatte R.

BMC Genomics. 2011 Feb 16;12:113. doi: 10.1186/1471-2164-12-113.

11.

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.

12.

OrchidBase: a collection of sequences of the transcriptome derived from orchids.

Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, Tsai WC, Chen HH.

Plant Cell Physiol. 2011 Feb;52(2):238-43. doi: 10.1093/pcp/pcq201. Epub 2011 Jan 17.

PMID:
21245031
13.

DBM-DB: the diamondback moth genome database.

Tang W, Yu L, He W, Yang G, Ke F, Baxter SW, You S, Douglas CJ, You M.

Database (Oxford). 2014 Jan 16;2014:bat087. doi: 10.1093/database/bat087. Print 2014.

14.

CLIPdb: a CLIP-seq database for protein-RNA interactions.

Yang YC, Di C, Hu B, Zhou M, Liu Y, Song N, Li Y, Umetsu J, Lu ZJ.

BMC Genomics. 2015 Feb 5;16:51. doi: 10.1186/s12864-015-1273-2.

15.

EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration.

Forment J, Gilabert F, Robles A, Conejero V, Nuez F, Blanca JM.

BMC Bioinformatics. 2008 Jan 7;9:5. doi: 10.1186/1471-2105-9-5.

16.

Integrative analysis of independent transcriptome data for rare diseases.

Zhang Z, Hailat Z, Falk MJ, Chen XW.

Methods. 2014 Oct 1;69(3):315-25. doi: 10.1016/j.ymeth.2014.06.003. Epub 2014 Jun 27.

17.

PhenoDigm: analyzing curated annotations to associate animal models with human diseases.

Smedley D, Oellrich A, Köhler S, Ruef B; Sanger Mouse Genetics Project, Westerfield M, Robinson P, Lewis S, Mungall C.

Database (Oxford). 2013 May 9;2013:bat025. doi: 10.1093/database/bat025. Print 2013.

18.

Verifying the markers of ovarian cancer using RNA-seq data.

Liu T, Yu N, Ding F, Wang S, Li S, Zhang X, Sun X, Chen Y, Liu P.

Mol Med Rep. 2015 Jul;12(1):1125-30. doi: 10.3892/mmr.2015.3489. Epub 2015 Mar 13.

PMID:
25776533
19.

SplicerAV: a tool for mining microarray expression data for changes in RNA processing.

Robinson TJ, Dinan MA, Dewhirst M, Garcia-Blanco MA, Pearson JL.

BMC Bioinformatics. 2010 Feb 25;11:108. doi: 10.1186/1471-2105-11-108.

20.

CGPredictor: a systematic integrated analytic tool for mining and examining genome-scale cancer independent prognostic epigenetic marker panels.

Cheng WS, Chiang JH.

BMC Syst Biol. 2013;7 Suppl 6:S10. doi: 10.1186/1752-0509-7-S6-S10. Epub 2013 Dec 13.

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