Toxicology. 2010 Feb 9;268(3):143-6. Epub 2009 Sep 27.

Application of connectivity mapping in predictive toxicology based on gene-expression similarity.

Source

Medical Research Council Toxicology Unit, University of Leicester, Systems Toxicology Group, Lancaster Road, Leicester, LE1 9HN, UK.

Abstract

Connectivity mapping is the process of establishing connections between different biological states using gene-expression profiles or signatures. There are a number of applications but in toxicology the most pertinent is for understanding mechanisms of toxicity. In its essence the process involves comparing a query gene signature generated as a result of exposure of a biological system to a chemical to those in a database that have been previously derived. In the ideal situation the query gene-expression signature is characteristic of the event and will be matched to similar events in the database. Key criteria are therefore the means of choosing the signature to be matched and the means by which the match is made. In this article we explore these concepts with examples applicable to toxicology.

PMID:: 19788908; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances, Grant Support

Publication Types

MeSH Terms

Substances

Receptors, Estrogen

Grant Support

Medical Research Council/United Kingdom

LinkOut - more resources

Full Text Sources

Supplemental Content

Save items

Related citations in PubMed

Review Recent applications of DNA microarray technology to toxicology and ecotoxicology. [Environ Health Perspect. 2006]
Review Recent applications of DNA microarray technology to toxicology and ecotoxicology.
Lettieri T. Environ Health Perspect. 2006 Jan; 114(1):4-9.
sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures. [BMC Bioinformatics. 2009]
sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures.
Zhang SD, Gant TW. BMC Bioinformatics. 2009 Jul 31; 10:236. Epub 2009 Jul 31.
Review Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology. [Toxicol Sci. 2001]
Review Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology.
Fielden MR, Zacharewski TR. Toxicol Sci. 2001 Mar; 60(1):6-10.
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.
Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes. [Pharmacogenomics J. 2010]
Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes.
Shi W, Bessarabova M, Dosymbekov D, Dezso Z, Nikolskaya T, Dudoladova M, Serebryiskaya T, Bugrim A, Guryanov A, Brennan RJ, et al. Pharmacogenomics J. 2010 Aug; 10(4):310-23.

See reviews... See all...

Cited by 1 PubMed Central article

Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping. [PLoS One. 2011]
Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping.
McArt DG, Zhang SD. PLoS One. 2011 Jan 31; 6(1):e16382. Epub 2011 Jan 31.

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.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Application of connectivity mapping in predictive toxicology based on gene-expre...
Application of connectivity mapping in predictive toxicology based on gene-expression similarity.
Toxicology. 2010 Feb 9 ;268(3):143-6. Epub 2009 Sep 27 .

PubMed
Chamomile, a novel and selective COX-2 inhibitor with anti-inflammatory activity...
Chamomile, a novel and selective COX-2 inhibitor with anti-inflammatory activity.
Life Sci. 2009 Nov 4 ;85(19-20):663-9. Epub 2009 Sep 27 .

PubMed
Mechanism of amyloidogenesis: nucleation-dependent fibrillation versus double-co...
Mechanism of amyloidogenesis: nucleation-dependent fibrillation versus double-concerted fibrillation.
BMB Rep. 2009 Sep 30 ;42(9):541-51.

PubMed
Reemergence of strongyloidiasis, northern Italy.
Reemergence of strongyloidiasis, northern Italy.
Emerg Infect Dis. 2009 Sep ;15(9):1531-3.

PubMed
Increasing incidence of zygomycosis (mucormycosis), France, 1997-2006.
Increasing incidence of zygomycosis (mucormycosis), France, 1997-2006.
Emerg Infect Dis. 2009 Sep ;15(9):1395-401.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: