Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.
Nat Protoc
; 6(12): 1860-9, 2011 Nov 03.
Article
en En
| MEDLINE
| ID: mdl-22051799
The transcription factor affinity prediction (TRAP) method calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the putative target genes of a given factor. This protocol covers two other applications: (i) determining which transcription factors have the highest affinity in a set of sequences (illustrated with chromatin immunoprecipitation-sequencing (ChIP-seq) peaks), and (ii) finding which factor is the most affected by a regulatory single-nucleotide polymorphism. The protocol describes how to use the TRAP web tools to address these questions, and it also presents a way to run TRAP on random control sequences to better estimate the significance of the results. All of the tools are fully available online and do not need any additional installation. The complete protocol takes about 45 min, but each individual tool runs in a few minutes.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Factores de Transcripción
/
Programas Informáticos
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Polimorfismo de Nucleótido Simple
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Inmunoprecipitación de Cromatina
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Nat Protoc
Año:
2011
Tipo del documento:
Article
País de afiliación:
Alemania
Pais de publicación:
Reino Unido