Drug Discov Today. 2005 May 15;10(10):727-34.

Bioinformatic methods for integrating whole-genome expression results into cellular networks.

Source

Department of Pharmacology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy. duccio.cavalieri@unifi.it

Abstract

Extracting a comprehensive overview from the huge amount of information arising from whole-genome analyses is a significant challenge. This review critically surveys the state of the art methods that are used to connect information from functional genomic studies to biological function. Cluster analysis methods for inferring the correlation between genes are discussed, as are the methods for integrating gene expression information with existing information on biological pathways and the methods that combine cluster analysis with biological information to reconstruct novel biological networks.

PMID:: 15896686; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms

Publication Types

Review

MeSH Terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

Review Where are we in genomics? [J Physiol Pharmacol. 2005]
Review Where are we in genomics?
Hocquette JF. J Physiol Pharmacol. 2005 Jun; 56 Suppl 3:37-70.
Review Computational identification of cellular networks and pathways. [Mol Biosyst. 2007]
Review Computational identification of cellular networks and pathways.
Markowetz F, Troyanskaya OG. Mol Biosyst. 2007 Jul; 3(7):478-82. Epub 2007 May 14.
Review Genomic approaches for reconstructing gene networks. [Pharmacogenomics. 2005]
Review Genomic approaches for reconstructing gene networks.
Lee NH. Pharmacogenomics. 2005 Apr; 6(3):245-58.
Review Dissecting the transcription networks of a cell using computational genomics. [Curr Opin Genet Dev. 2003]
Review Dissecting the transcription networks of a cell using computational genomics.
Li H, Wang W. Curr Opin Genet Dev. 2003 Dec; 13(6):611-6.
Review Computational approaches to analysis of DNA microarray data. [Yearb Med Inform. 2006]
Review Computational approaches to analysis of DNA microarray data.
Quackenbush J. Yearb Med Inform. 2006; :91-103.

See reviews... See all...

Cited by 11 PubMed Central articles

Systems biology of fungal infection. [Front Microbiol. 2012]
Systems biology of fungal infection.
Horn F, Heinekamp T, Kniemeyer O, Pollmächer J, Valiante V, Brakhage AA. Front Microbiol. 2012; 3:108. Epub 2012 Apr 2.
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. [Bioinformatics. 2011]
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.
Beltrame L, Calura E, Popovici RR, Rizzetto L, Guedez DR, Donato M, Romualdi C, Draghici S, Cavalieri D. Bioinformatics. 2011 Aug 1; 27(15):2127-33. Epub 2011 Jun 7.
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. [BMC Syst Biol. 2010]
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems.
Raza S, McDerment N, Lacaze PA, Robertson K, Watterson S, Chen Y, Chisholm M, Eleftheriadis G, Monk S, O'Sullivan M, et al. BMC Syst Biol. 2010 May 14; 4:63. Epub 2010 May 14.

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

Bioinformatic methods for integrating whole-genome expression results into cellu...
Bioinformatic methods for integrating whole-genome expression results into cellular networks.
Drug Discov Today. 2005 May 15 ;10(10):727-34.

PubMed
Biochemical and genetic characterization of four cases of hereditary coproporphy...
Biochemical and genetic characterization of four cases of hereditary coproporphyria in Spain.
Mol Genet Metab. 2005 Jun ;85(2):160-3. Epub 2005 Feb 25 .

PubMed
Usefulness of procalcitonin in the early detection of infection after thoracic s...
Usefulness of procalcitonin in the early detection of infection after thoracic surgery.
Eur J Cardiothorac Surg. 2005 Jun ;27(6):1074-8. Epub 2005 Apr 25 .

PubMed
The use of selected interventions in monitoring primary health care implementati...
The use of selected interventions in monitoring primary health care implementation in rural Nigeria.
Scand J Prim Health Care. 1992 Mar ;10(1):30-5.

PubMed
A comparison of fentanyl-propofol with a ketamine-propofol combination for sedat...
A comparison of fentanyl-propofol with a ketamine-propofol combination for sedation during endometrial biopsy.
J Clin Anesth. 2005 May ;17(3):187-90.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: