factorbook: MotifDb object containing motif information from around the...

In Simon-Coetzee/motifBreakR: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

MotifDb object containing motif information from around the genomic regions bound by 119 human transcription factors in Factorbook.

Description

From the abstract: "Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones. The motif sites (TF binding sites) are highly conserved evolutionarily and show distinct footprints upon DNase I digestion. We frequently detected secondary motifs in addition to the canonical motifs of the TFs, indicating tethered binding and cobinding between multiple TFs. We observed significant position and orientation preferences between many cobinding TFs. Genes specifically expressed in a cell line are often associated with a greater occurrence of nearby TF binding in that cell line. We observed cell-line-specific secondary motifs that mediate the binding of the histone deacetylase HDAC2 and the enhancer-binding protein EP300. TF binding sites are located in GC-rich, nucleosome-depleted, and DNase I sensitive regions, flanked by well-positioned nucleosomes, and many of these features show cell type specificity. The GC-richness may be beneficial for regulating TF binding because, when unoccupied by a TF, these regions are occupied by nucleosomes in vivo. We present the results of our analysis in a TF-centric web repository Factorbook (http://factorbook.org) and will continually update this repository as more ENCODE data are generated."

Usage

factorbook

Format

MotifDb object of length 79; to access metadata use mcols(factorbook)

providerName

Name listed in meme output of 'Supp TableS2.pdf' for the citation indicated below

providerId

Same as providerName

dataSource

"FactorBook"

geneSymbol

NA these motifs don't have a direct 1 to 1 relationship with a transcription factor

geneId

NA

geneIdType

NA

proteinId

NA

proteinIdType

NA

organism

"Hsapiens"

sequenceCount

NA

bindingSequence

Consensus sequence for the motif

bindingDomain

NA

tfFamily

NA

experimentType

NA

pubmedID

"22955990" see Source for more details

Details

Load with data(factorbook)

Value

MotifList-class object

Source

J Wang, J Zhuang, S Iyer, XY Lin, et al. (2012) Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research, 22 (9), 1798-1812, doi:10.1101/gr.139105.112

See Also

http://factorbook.org

Examples

data(factorbook)
factorbook

Simon-Coetzee/motifBreakR documentation built on Aug. 6, 2024, 5:17 a.m.