Genome-wide prediction and analysis of function-specific transcription factor binding sites.
In Silico Biol
; 4(4): 395-410, 2004.
Article
em En
| MEDLINE
| ID: mdl-15506990
ABSTRACT
DNA-binding transcription factors play a central role in transcription regulation, and the annotation of transcription-factor binding sites in upstream regions of human genes is essential for building a genome-wide regulatory network. We describe methodology to accurately predict the transcription-factor binding sites in the proximal-promoter region of function-specific genes. In order to increase the accuracy of transcription factor binding-site prediction, we rely on recent genome sequence data, known transcription factor binding-site matrices, and Gene Ontology biological-function-based gene classification. Using TRANSFAC position-frequency matrices, we detected individual and cooperating transcription-factor binding sites in proximal promoters of ENSEMBL annotated human genes. We used the over representation of detected binding sites in the proximal promoters as compared to the second exons to control specificity. We confirmed the majority of transcription-factor binding sites predicted in proximal promoters of immune-response genes with evidence from existing literature. We validated the predicted cooperation between transcription factors NF-kappa B and IRF in the regulation of gene expression with microarray transcript profiling data and literature-derived protein-protein interaction network. We also identified over-represented individual and pairs of transcription-factor binding sites in the proximal promoters of each Gene Ontology biological-process gene group. Our tools and analysis provide a new resource for deciphering transcription regulation in different biological paradigms.
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Base de dados:
MEDLINE
Assunto principal:
Fatores de Transcrição
/
Genoma Humano
/
Regiões Promotoras Genéticas
/
Biologia Computacional
/
Genômica
/
Proteínas de Ligação a DNA
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Limite:
Humans
Idioma:
En
Revista:
In Silico Biol
Assunto da revista:
BIOLOGIA MOLECULAR
Ano de publicação:
2004
Tipo de documento:
Article
País de afiliação:
Estados Unidos