Warning: The NCBI web site requires JavaScript to function. more...

My NCBI Sign In

Genome Biol. 2010;11(2):R23. Epub 2010 Feb 26.

Identification of functional modules that correlate with phenotypic difference: the influence of network topology.

Hung JH, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C.

Source

Bioinformatics Program, Boston University, 24 Cummington Street, Boston, MA 02215, USA.

Abstract

One of the important challenges to post-genomic biology is relating observed phenotypic alterations to the underlying collective alterations in genes. Current inferential methods, however, invariably omit large bodies of information on the relationships between genes. We present a method that takes account of such information - expressed in terms of the topology of a correlation network - and we apply the method in the context of current procedures for gene set enrichment analysis.

PMID:: 20187943; [PubMed - indexed for MEDLINE]
PMCID: PMC2872883

Free PMC Article

Images from this publication.See all images (4) Free text

Publication Types, MeSH Terms, Grant Support

Publication Types

Research Support, N.I.H., Extramural

MeSH Terms

Grant Support

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Libraries

LinkOut Holdings

Supplemental Content

Click here to read

Click here to read

Related citations

Finding microRNA regulatory modules in human genome using rule induction. [BMC Bioinformatics. 2008]
Finding microRNA regulatory modules in human genome using rule induction.
Tran DH, Satou K, Ho TB. BMC Bioinformatics. 2008 Dec 12; 9 Suppl 12:S5. Epub 2008 Dec 12.
Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization. [Bioinformatics. 2009]
Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization.
Yang X, Zhou Y, Jin R, Chan C. Bioinformatics. 2009 Sep 1; 25(17):2236-43. Epub 2009 Jun 19.
Reverse engineering module networks by PSO-RNN hybrid modeling. [BMC Genomics. 2009]
Reverse engineering module networks by PSO-RNN hybrid modeling.
Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW. BMC Genomics. 2009 Jul 7; 10 Suppl 1:S15. Epub 2009 Jul 7.
Review Functional models for large-scale gene regulation networks: realism and fiction. [Mol Biosyst. 2009]
Review Functional models for large-scale gene regulation networks: realism and fiction.
Lagomarsino MC, Bassetti B, Castellani G, Remondini D. Mol Biosyst. 2009 Apr; 5(4):335-44. Epub 2009 Jan 30.
Review Inferring regulatory networks. [Front Biosci. 2008]
Review Inferring regulatory networks.
Li H, Xuan J, Wang Y, Zhan M. Front Biosci. 2008 Jan 1; 13:263-75. Epub 2008 Jan 1.

See reviews... See all...

Cited by 1 PubMed Central article

Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data. [Pac Symp Biocomput. 2011]
Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data.
Turcan S, Vetter DE, Maron JL, Wei X, Slonim DK. Pac Symp Biocomput. 2011; :50-61.

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

Identification of functional modules that correlate with phenotypic difference: ...
Identification of functional modules that correlate with phenotypic difference: the influence of network topology.
Genome Biol. 2010 ;11(2):R23. Epub 2010 Feb 26 .

PubMed
Flexible sequence similarity searching with the FASTA3 program package.
Flexible sequence similarity searching with the FASTA3 program package.
Methods Mol Biol. 2000 ;132:185-219.

PubMed
Human centromeres and neocentromeres show identical distribution patterns of >20...
Human centromeres and neocentromeres show identical distribution patterns of >20 functionally important kinetochore-associated proteins.
Hum Mol Genet. 2000 Jan 22 ;9(2):175-85.

PubMed
Systematic variation in gene expression patterns in human cancer cell lines.
Systematic variation in gene expression patterns in human cancer cell lines.
Nat Genet. 2000 Mar ;24(3):227-35.

PubMed
The WASP and WAVE family proteins.
The WASP and WAVE family proteins.
Genome Biol. 2009 ;10(6):226. Epub 2009 Jun 15 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

You are here: NCBI > Literature > PubMed

Write to the Help Desk