Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W406-10. Epub 2008 Apr 28.

CoPub: a literature-based keyword enrichment tool for microarray data analysis.

Frijters R, Heupers B, van Beek P, Bouwhuis M, van Schaik R, de Vlieg J, Polman J, Alkema W.

Source

Computational Drug Discovery (CDD),, Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

Abstract

Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. CoPub is freely accessible at http://services.nbic.nl/cgi-bin/copub/CoPub.pl.

PMID:: 18442992; [PubMed - indexed for MEDLINE]
PMCID:: PMC2447728

Free PMC Article

Images from this publication.See all images (2) Free text

Publication Types, MeSH Terms

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

LinkOut - more resources

Full Text Sources

Supplemental Content

Save items

Related citations in PubMed

CoPub Mapper: mining MEDLINE based on search term co-publication. [BMC Bioinformatics. 2005]
CoPub Mapper: mining MEDLINE based on search term co-publication.
Alako BT, Veldhoven A, van Baal S, Jelier R, Verhoeven S, Rullmann T, Polman J, Jenster G. BMC Bioinformatics. 2005 Mar 11; 6:51. Epub 2005 Mar 11.
CoPub update: CoPub 5.0 a text mining system to answer biological questions. [Nucleic Acids Res. 2011]
CoPub update: CoPub 5.0 a text mining system to answer biological questions.
Fleuren WW, Verhoeven S, Frijters R, Heupers B, Polman J, van Schaik R, de Vlieg J, Alkema W. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W450-4. Epub 2011 May 27.
GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. [BMC Genomics. 2009]
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. Epub 2009 Sep 3.
Review Pre-processing of microarray data and analysis of differential expression. [Methods Mol Biol. 2008]
Review Pre-processing of microarray data and analysis of differential expression.
Durinck S. Methods Mol Biol. 2008; 452:89-110.
Review [Bibliographic medical research using MEDLINE-PubMed. A practical approach based on examples]. [Nephrol Ther. 2007]
Review [Bibliographic medical research using MEDLINE-PubMed. A practical approach based on examples].
Eveillard P, Hannedouche T. Nephrol Ther. 2007 Dec; 3(7):475-85. Epub 2007 Sep 6.

See reviews... See all...

Cited by 9 PubMed Central articles

GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation. [Adv Bioinformatics. 2011]
GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation.
Gosink M, Khuri S, Valdes C, Jiang Z, Tsinoremas NF. Adv Bioinformatics. 2011; 2011:271563. Epub 2011 Dec 13.
Discovering and visualizing indirect associations between biomedical concepts. [Bioinformatics. 2011]
Discovering and visualizing indirect associations between biomedical concepts.
Tsuruoka Y, Miwa M, Hamamoto K, Tsujii J, Ananiadou S. Bioinformatics. 2011 Jul 1; 27(13):i111-9.
CoPub update: CoPub 5.0 a text mining system to answer biological questions. [Nucleic Acids Res. 2011]
CoPub update: CoPub 5.0 a text mining system to answer biological questions.
Fleuren WW, Verhoeven S, Frijters R, Heupers B, Polman J, van Schaik R, de Vlieg J, Alkema W. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W450-4. Epub 2011 May 27.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

CoPub: a literature-based keyword enrichment tool for microarray data analysis.
CoPub: a literature-based keyword enrichment tool for microarray data analysis.
Nucleic Acids Res. 2008 Jul 1 ;36(Web Server issue):W406-10. Epub 2008 Apr 28 .

PubMed
CRISPRcompar: a website to compare clustered regularly interspaced short palindr...
CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.
Nucleic Acids Res. 2008 Jul 1 ;36(Web Server issue):W145-8. Epub 2008 Apr 28 .

PubMed
Regulation of intra-S phase checkpoint by ionizing radiation (IR)-dependent and ...
Regulation of intra-S phase checkpoint by ionizing radiation (IR)-dependent and IR-independent phosphorylation of SMC3.
J Biol Chem. 2008 Jul 11 ;283(28):19176-83. Epub 2008 Apr 28 .

PubMed
Adult autopsy case with marked myositis ossificans: association with repetitive ...
Adult autopsy case with marked myositis ossificans: association with repetitive physical assault and battery.
Leg Med (Tokyo). 2008 Sep ;10(5):274-6. Epub 2008 Apr 28 .

PubMed
A novel locus for dilated cardiomyopathy maps to canine chromosome 8.
A novel locus for dilated cardiomyopathy maps to canine chromosome 8.
Genomics. 2008 Jun ;91(6):517-21. Epub 2008 Apr 28 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: