An application of machine learning algorithms enables prediction of the functional context of transcription factor binding sites in the human genome

Borlak, Jürgen

Kel, Alexander E

Matys, Volker

Niehof, Monika

Zemlin, Rüdiger

English

PubMed

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)4 alpha binding sites and significantly improved an overall recognition of faithful HNF4 alpha targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor

Kel, A.E.

Niehof, M.

Matys, V.

Zemlin, R.

Borlak, J.

Fraunhofer-ePrints

Genome wide prediction of HNF4 alpha functional binding sites by the use of local and global sequence context

Alexander E Kel

Monika Niehof

Volker Matys

Rüdiger Zemlin

Jürgen Borlak

Springer - Publisher Connector

Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

Crossref

A discriminative model for identifying spatial cis-regulatory modules.

A novel computational approach for the prediction of networked transcription factors of aryl hydrocarbon-receptorregulated genes. Mol Pharmacol

Aberrant intestinal expression and allelic variants of mucin genes associated with inflammatory bowel disease.

Activation of the tyrosine aminotransferase gene is dependent on synergy between liverspecific and hormone-responsive elements.

Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res

Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome.

BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput

Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics

Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol

Curr Opin Genet Dev

De Moor B: Computational detection of cis-regulatory modules. Bioinformatics

Decaux JF: The coactivator PGC-1 is involved in the regulation of the liver carnitine palmitoyltransferase I gene expression by cAMP in combination with HNF4 alpha and cAMP-response elementbinding protein (CREB).

Deineko IV, Wingender E: TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res

E: Finding transcription factor binding site combinations in the yeast genome.

Fickett JW: Identification of regulatory regions which confer muscle-specific gene expression.

Fraenkel E: Tissuespecific transcriptional regulation has diverged significantly between human and mouse. Nat Genet

Functional interactions between nuclear receptors recognizing a common sequence element, the direct repeat motif spaced by one nucleotide (DR-1).

H: Analysis of gene expression profile induced by hepatocyte nuclear factor 4alpha in hepatoma cells using an oligonucleotide microarray.

Hepatocyte nuclear factor 4alpha orchestrates expression of cell adhesion proteins during the epithelial transformation of the developing liver. Proc Natl Acad Sci USA

HF: The orphan receptor hepatic nuclear factor 4 functions as a transcriptional activator for tissue-specific and hypoxiaspecific erythropoietin gene expression and is antagonized by EAR3/COUP-TF1. Mol Cell Biol

Hirano T: Identification of a novel interleukin-6 response element containing an Ets-binding site and a CRE-like site in the junB promoter. Mol Cell Biol

Identifying transcription factor binding sites through Markov chain optimization. Bioinformatics 2002, 18(Suppl 2):S100-S109.

JW: Estrogen receptor, a common interaction partner for a subset of nuclear receptors. Mol Endocrinol

Kaestner KH: Expansion of adult β-cell mass in response to increased metabolic demand is dependent on HNF-4α. Genes Dev

Kel A: Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. Nucleic Acids Res

Kel A: Whole genome human/mouse phylogenetic footprinting of potential transcription regulatory signals. Pac Symp Biocomput

Kel AE: Automatic annotation of genomic regulatory sequences by searching for composite clusters. Pac Symp Biocomput

Kolchanov NA: SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Comput Appl Biosci

Liver-enriched transcription factors in liver function and development. Part I: the hepatocyte nuclear factor network and liver-specific gene expression. Pharmacol Rev

Muscle actin genes: a first step towards computational classification of tissue specific promoters.

Pevzner PA: Finding composite regulatory patterns in DNA sequences. Bioinformatics 2002, 18(Suppl 1):S354-S363.

PJ: A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data - a case study using E2F1. Genome Res

PJ: ATF and Jun transcription factors, acting through an Ets/CRE promoter module, mediate lipopolysaccharide inducibility of the chemokine RANTES in monocytic Mono Mac 6 cells.

PJ: Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells.

Potapov AP: Integrative content-driven concepts for bioinformatics &quot;beyond the cell&quot;.

RA: Control of pancreas and liver gene expression by HNF transcription factors. Science

RG: Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res

RSK4 and PAK5 are novel candidate genes in diabetic rat kidney and brain. Mol Pharmacol

Ryffel GU: HNF4alpha reduces proliferation of kidney cells and affects genes deregulated in renal cell carcinoma. Oncogene

Ryffel GU: Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4alpha and HNF1beta in a pancreatic beta-cell line. Nucleic Acids Res

S: Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res

Siggia ED: A probabilistic method to detect regulatory modules. Bioinformatics

Stormo GD: Identifying target sites for cooperatively binding factors. Bioinformatics

UA: NUBIScan, an in silico approach for prediction of nuclear receptor response elements. Mol Endocrinol

Wadelius C: Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays. Hum Mol Genet

Wasserman WW: Prediction of nuclear hormone receptor response elements. Mol Endocrinol

Wingender E: Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations. Bioinformatics

Wingender E: Construction of predictive promoter models on the example of antibacterial response of human epithelial cells. Theor Biol Med Model

Wingender E: Evaluating phylogenetic footprinting for human-rodent comparisons. Bioinformatics

Wingender E: MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res

Wingender E: Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells.

Wingender E: TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res

Wingender E: TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes. Nucleic Acids Res

Zhang MQ: Computer-assisted identification of cell cyclerelated genes: new targets for E2F transcription factors.

Zhang MQ: Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2374721

Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

Abstract

Similar works

Full text

Available Versions

Fraunhofer-ePrints

Springer - Publisher Connector

Crossref