Target analysis by integration of transcriptome and ChIP-seq data with BETA View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-12

AUTHORS

Su Wang, Hanfei Sun, Jian Ma, Chongzhi Zang, Chenfei Wang, Juan Wang, Qianzi Tang, Clifford A Meyer, Yong Zhang, X Shirley Liu

ABSTRACT

The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression. Several recently published methods combine transcription factor (TF) binding and gene expression for target prediction, but few of them provide an efficient software package for the community. Binding and expression target analysis (BETA) is a software package that integrates ChIP-seq of TFs or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (i) to predict whether the factor has activating or repressive function; (ii) to infer the factor's target genes; and (iii) to identify the motif of the factor and its collaborators, which might modulate the factor's activating or repressive function. Here we describe the implementation and features of BETA to demonstrate its application to several data sets. BETA requires ~1 GB of RAM, and the procedure takes 20 min to complete. BETA is available open source at http://cistrome.org/BETA/. More... »

PAGES

2502-2515

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nprot.2013.150

DOI

http://dx.doi.org/10.1038/nprot.2013.150

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1022717163

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24263090


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nprot.2013.150'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nprot.2013.150'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nprot.2013.150'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nprot.2013.150'


 

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