Genome Inform. 2007;19:61-72.

A conservative parametric approach to motif significance analysis.

Source

Department of Computer Science, Cornell University, Ithaca, NY, USA.

Abstract

We suggest a novel, parametric, approach to estimating the significance of the output of motif finders. Specifically, we rely on the good fit we observe between the 3-parameters Gamma family and the null distribution of motif scores. This fit was observed across multiple motif finders, background models and scoring functions. Under this parametric assumption we compute and show the utility of a conservative confidence interval for the p-value of the observed score. Since our method relies on the 3-parameters Gamma fit it should be applicable to a variety of finders.

PMID:: 18546505; [PubMed - indexed for MEDLINE]

MeSH Terms, Substances

MeSH Terms

Substances

Transcription Factors

LinkOut - more resources

Other Literature Sources

COS Scholar Universe

Supplemental Content

Related citations

Calibrating E-values for hidden Markov models using reverse-sequence null models. [Bioinformatics. 2005]
Calibrating E-values for hidden Markov models using reverse-sequence null models.
Karplus K, Karchin R, Shackelford G, Hughey R. Bioinformatics. 2005 Nov 15; 21(22):4107-15. Epub 2005 Aug 25.
Variable structure motifs for transcription factor binding sites. [BMC Genomics. 2010]
Variable structure motifs for transcription factor binding sites.
Reid JE, Evans KJ, Dyer N, Wernisch L, Ott S. BMC Genomics. 2010 Jan 14; 11:30. Epub 2010 Jan 14.
A correlated motif approach for finding short linear motifs from protein interaction networks. [BMC Bioinformatics. 2006]
A correlated motif approach for finding short linear motifs from protein interaction networks.
Tan SH, Hugo W, Sung WK, Ng SK. BMC Bioinformatics. 2006 Nov 16; 7:502. Epub 2006 Nov 16.
Review Discovering sequence motifs. [Methods Mol Biol. 2008]
Review Discovering sequence motifs.
Bailey TL. Methods Mol Biol. 2008; 452:231-51.
Review Structure-based ab initio prediction of transcription factor-binding sites. [Methods Mol Biol. 2009]
Review Structure-based ab initio prediction of transcription factor-binding sites.
Liu LA, Bader JS. Methods Mol Biol. 2009; 541:23-41.

See reviews... See all...

Recent activity

Clear Turn Off Turn On

A conservative parametric approach to motif significance analysis.
A conservative parametric approach to motif significance analysis.
Genome Inform. 2007 ;19:61-72.

PubMed
Metabolic effects of diets differing in glycaemic index depend on age and endoge...
Metabolic effects of diets differing in glycaemic index depend on age and endogenous glucose-dependent insulinotrophic polypeptide in mice.
Diabetologia. 2009 Oct ;52(10):2159-68. Epub 2009 Jul 31 .

PubMed
Identification of phosphorylation sites in AMP-activated protein kinase (AMPK) f...
Identification of phosphorylation sites in AMP-activated protein kinase (AMPK) for upstream AMPK kinases and study of their roles by site-directed mutagenesis.
J Biol Chem. 2003 Aug 1 ;278(31):28434-42. Epub 2003 May 21 .

PubMed
The AMP-activated protein kinase cascade--a unifying system for energy control.
The AMP-activated protein kinase cascade--a unifying system for energy control.
Trends Biochem Sci. 2004 Jan ;29(1):18-24.

PubMed
Post-translational modifications of the beta-1 subunit of AMP-activated protein ...
Post-translational modifications of the beta-1 subunit of AMP-activated protein kinase affect enzyme activity and cellular localization.
Biochem J. 2001 Mar 1 ;354(Pt 2):275-83.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to:

A conservative parametric approach to motif significance analysis.

Source

Abstract

MeSH Terms, Substances

MeSH Terms

Substances

LinkOut - more resources

Other Literature Sources

Supplemental Content

Related citations

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information