Clin Lab Med. 2008 Mar;28(1):127-43, viii.

Data mining for biomarker development: a review of tissue specificity analysis.

Source

Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Stabile 2-50, Rochester, MN 55905, USA. klee.eric@mayo.edu

Abstract

Novel biomarker development requires a significant resource commitment to translate candidate markers into clinical assays. Consequently, it is imperative high quality candidates are selected early in a biomarker development program. High throughput gene expression data are routinely used to identify transcripts differentially expressed in diseased versus normal samples. Data-mining Expressed Sequence Tag, Serial Analysis of Gene Expression, Massively Parallel Signature Sequencing, and microarray expression databases can provide additional information on the expression of candidate biomarkers across multiple tissues, organs, and disease states. From this information, quantitative measures of tissue-specific gene specificity are computed and used to guide candidate biomarker selection.

PMID:: 18194723; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

Review

MeSH Terms

Substances

Biological Markers

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Supplemental Content

Save items

Related citations in PubMed

Knowledge-guided multi-scale independent component analysis for biomarker identification. [BMC Bioinformatics. 2008]
Knowledge-guided multi-scale independent component analysis for biomarker identification.
Chen L, Xuan J, Wang C, Shih IeM, Wang Y, Zhang Z, Hoffman E, Clarke R. BMC Bioinformatics. 2008 Oct 6; 9:416. Epub 2008 Oct 6.
Integration of text- and data-mining using ontologies successfully selects disease gene candidates. [Nucleic Acids Res. 2005]
Integration of text- and data-mining using ontologies successfully selects disease gene candidates.
Tiffin N, Kelso JF, Powell AR, Pan H, Bajic VB, Hide WA. Nucleic Acids Res. 2005; 33(5):1544-52. Epub 2005 Mar 14.
Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies. [BMC Genomics. 2009]
Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies.
Hornshøj H, Bendixen E, Conley LN, Andersen PK, Hedegaard J, Panitz F, Bendixen C. BMC Genomics. 2009 Jan 19; 10:30. Epub 2009 Jan 19.
Review Molecular signature analysis: using the myocardial transcriptome as a biomarker in cardiovascular disease. [Trends Cardiovasc Med. 2005]
Review Molecular signature analysis: using the myocardial transcriptome as a biomarker in cardiovascular disease.
Kittleson MM, Hare JM. Trends Cardiovasc Med. 2005 May; 15(4):130-8.
Review Biomarkers in aquatic plants: selection and utility. [Rev Environ Contam Toxicol. 2009]
Review Biomarkers in aquatic plants: selection and utility.
Brain RA, Cedergreen N. Rev Environ Contam Toxicol. 2009; 198:49-109.

See reviews... See all...

Cited by 4 PubMed Central articles

HOMER: a human organ-specific molecular electronic repository. [BMC Bioinformatics. 2011]
HOMER: a human organ-specific molecular electronic repository.
Zhang F, Chen JY. BMC Bioinformatics. 2011 Oct 18; 12 Suppl 10:S4. Epub 2011 Oct 18.
Microarray data integration for genome-wide analysis of human tissue-selective gene expression. [BMC Genomics. 2010]
Microarray data integration for genome-wide analysis of human tissue-selective gene expression.
Wang L, Srivastava AK, Schwartz CE. BMC Genomics. 2010 Nov 2; 11 Suppl 2:S15. Epub 2010 Nov 2.
Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach. [Bioinformatics. 2009]
Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach.
Van Deun K, Hoijtink H, Thorrez L, Van Lommel L, Schuit F, Van Mechelen I. Bioinformatics. 2009 Oct 1; 25(19):2588-94. Epub 2009 Aug 11.

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

Recent activity

Clear Turn Off Turn On

Data mining for biomarker development: a review of tissue specificity analysis.
Data mining for biomarker development: a review of tissue specificity analysis.
Clin Lab Med. 2008 Mar ;28(1):127-43, viii.

PubMed
Is there a better way to biopsy the prostate? Prospects for a novel transrectal ...
Is there a better way to biopsy the prostate? Prospects for a novel transrectal systematic biopsy approach.
Urology. 2007 Dec ;70(6 Suppl):22-6.

PubMed
Effect of fatigue on psychomotor and cognitive skills.
Effect of fatigue on psychomotor and cognitive skills.
Am J Surg. 2008 Feb ;195(2):195-204.

PubMed
Double-blind, placebo-controlled trial of carisoprodol 250-mg tablets in the tre...
Double-blind, placebo-controlled trial of carisoprodol 250-mg tablets in the treatment of acute lower-back spasm.
Curr Med Res Opin. 2008 Feb ;24(2):551-8.

PubMed
Var transcription profiling of Plasmodium falciparum 3D7: assignment of cytoadhe...
Var transcription profiling of Plasmodium falciparum 3D7: assignment of cytoadherent phenotypes to dominant transcripts.
Malar J. 2008 Jan 14 ;7:14.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: