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

My NCBI Sign In

Result Filters

Genome Biol. 2008;9(2):R36. Epub 2008 Feb 21.

Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context.

Kel AE, Niehof M, Matys V, Zemlin R, Borlak J.

Source

BIOBASE GmbH, Halchtersche Str, 38304 Wolfenbüttel, Germany. ake@biobase.de

Abstract

We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome. We demonstrate that our method allowed de novo identification of hepatic nuclear factor (HNF)4alpha binding sites and significantly improved an overall recognition of faithful HNF4alpha targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor.

PMID:: 18291023; [PubMed - indexed for MEDLINE]
PMCID:: PMC2374721

Free PMC Article

Images from this publication.See all images (6) Free text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

Hepatocyte Nuclear Factor 4

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Supplemental Content

Icon for BioMed Central

Icon for PubMed Central

Save items

loading

Related citations in PubMed

Involvement of hepatocyte nuclear factor 4alpha in the different expression level between CYP2C9 and CYP2C19 in the human liver. [Drug Metab Dispos. 2006]
Involvement of hepatocyte nuclear factor 4alpha in the different expression level between CYP2C9 and CYP2C19 in the human liver.
Kawashima S, Kobayashi K, Takama K, Higuchi T, Furihata T, Hosokawa M, Chiba K. Drug Metab Dispos. 2006 Jun; 34(6):1012-8. Epub 2006 Mar 15.
A high resolution genome-wide scan of HNF4α recognition sites infers a regulatory gene network in colon cancer. [PLoS One. 2011]
A high resolution genome-wide scan of HNF4α recognition sites infers a regulatory gene network in colon cancer.
Weltmeier F, Borlak J. PLoS One. 2011; 6(7):e21667. Epub 2011 Jul 28.
Expression of the hepatic specific V1 messenger ribonucleic acid of the human growth hormone receptor gene is regulated by hepatic nuclear factor (HNF)-4alpha2 and HNF-4alpha8. [Mol Endocrinol. 2008]
Expression of the hepatic specific V1 messenger ribonucleic acid of the human growth hormone receptor gene is regulated by hepatic nuclear factor (HNF)-4alpha2 and HNF-4alpha8.
Goodyer CG, Rhani Z, Zheng H. Mol Endocrinol. 2008 Feb; 22(2):485-500. Epub 2007 Nov 8.
Review Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. [J Endocrinol. 2009]
Review Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing.
Hoffman BG, Jones SJ. J Endocrinol. 2009 Apr; 201(1):1-13. Epub 2009 Jan 9.
Review Regulation of hepatocyte nuclear factor 4 alpha-mediated transcription. [Drug Metab Pharmacokinet. 2008]
Review Regulation of hepatocyte nuclear factor 4 alpha-mediated transcription.
Gonzalez FJ. Drug Metab Pharmacokinet. 2008; 23(1):2-7.

See reviews... See all...

Cited by 4 PubMed Central articles

Genomics meets glycomics-the first GWAS study of human N-Glycome identifies HNF1α as a master regulator of plasma protein fucosylation. [PLoS Genet. 2010]
Genomics meets glycomics-the first GWAS study of human N-Glycome identifies HNF1α as a master regulator of plasma protein fucosylation.
Lauc G, Essafi A, Huffman JE, Hayward C, Knežević A, Kattla JJ, Polašek O, Gornik O, Vitart V, Abrahams JL, et al. PLoS Genet. 2010 Dec 23; 6(12):e1001256. Epub 2010 Dec 23.
Alterations in hepatic mRNA expression of phase II enzymes and xenobiotic transporters after targeted disruption of hepatocyte nuclear factor 4 alpha. [Toxicol Sci. 2010]
Alterations in hepatic mRNA expression of phase II enzymes and xenobiotic transporters after targeted disruption of hepatocyte nuclear factor 4 alpha.
Lu H, Gonzalez FJ, Klaassen C. Toxicol Sci. 2010 Dec; 118(2):380-90. Epub 2010 Oct 8.
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. [Genome Res. 2010]
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.
Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I. Genome Res. 2010 May; 20(5):565-77. Epub 2010 Apr 2.

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.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
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

Genome wide prediction of HNF4alpha functional binding sites by the use of local...
Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context.
Genome Biol. 2008 ;9(2):R36. Epub 2008 Feb 21 .

PubMed
Twenty-four-week safety and tolerability of nevirapine vs. abacavir in combinati...
Twenty-four-week safety and tolerability of nevirapine vs. abacavir in combination with zidovudine/lamivudine as first-line antiretroviral therapy: a randomized double-blind trial (NORA).
Trop Med Int Health. 2008 Jan ;13(1):6-16.

PubMed
Mutation screening of TGFBI in two Iranian Avellino corneal dystrophy pedigrees.
Mutation screening of TGFBI in two Iranian Avellino corneal dystrophy pedigrees.
Clin Experiment Ophthalmol. 2008 Jan-Feb ;36(1):26-30.

PubMed
Psychotherapy intervention to reduce depressive symptoms in patients with diabet...
Psychotherapy intervention to reduce depressive symptoms in patients with diabetic foot syndrome.
Diabet Med. 2008 Feb ;25(2):206-12.

PubMed
Efficacy of tadalafil once daily in men with diabetes mellitus and erectile dysf...
Efficacy of tadalafil once daily in men with diabetes mellitus and erectile dysfunction.
Diabet Med. 2008 Feb ;25(2):138-46.

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