encodemotif: MotifDb object containing motif information from the known and discovered
motifs for the ENCODE TF ChIP-seq datasets.
Description
From the abstract: "Recent advances in technology have led to a dramatic
increase in the number of available transcription factor ChIP-seq and
ChIP-chip data sets. Understanding the motif content of these data sets is an
important step in understanding the underlying mechanisms of regulation. Here
we provide a systematic motif analysis for 427 human ChIP-seq data sets using
motifs curated from the literature and also discovered de novo using five
established motif discovery tools. We use a systematic pipeline for
calculating motif enrichment in each data set, providing a principled way for
choosing between motif variants found in the literature and for flagging
potentially problematic data sets. Our analysis confirms the known
specificity of 41 of the 56 analyzed factor groups and reveals motifs of
potential cofactors. We also use cell type-specific binding to find factors
active in specific conditions. The resource we provide is accessible both for
browsing a small number of factors and for performing large-scale systematic
analyses. We provide motif matrices, instances and enrichments in each of the
ENCODE data sets. The motifs discovered here have been used in parallel
studies to validate the specificity of antibodies, understand cooperativity
between data sets and measure the variation of motif binding across
individuals and species."
Format
MotifDb object of length 2064; to access metadata
use mcols(encodemotif)
- providerName
- Name provided by ENCODE
- providerId
- Same as providerName
- dataSource
"ENCODE-motif"- geneSymbol
- Gene symbol for the transcription factor
- geneId
- Entrez gene id for the transcription factor
- geneIdType
"ENTREZ"- proteinId
- UNIPROT id for the transcription factor
- proteinIdType
"UNIPROT"- organism
"Hsapiens"- sequenceCount
NA not available- bindingSequence
- Consensus sequence for the motif
- bindingDomain
NA incomplete- tfFamily
NA incomplete- experimentType
- occurs in two forms: For motifs that were discovered in this study, the format is
cellType_source-LabMetadata:MotifFinder#Location for example H1-hESC_encode-Myers_seq_hsa_v041610.2_r1:MEME#2#Intergenic. For motifs that were "known" the format tends to be TF_source_sourceId for example AP1_jaspar_MA0099.2.
- pubmedID
"24335146" see Source for more details
Source
Pouya Kheradpour and Manolis Kellis (2013 December 13) Systematic
discovery and characterization of regulatory motifs in ENCODE TF binding
experiments. Nucleic Acids Research, doi:10.1093/nar/gkt1249Details
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