homer: MotifDb object containing motif information from motif databases included in
HOMER.
Description
From the website: "Homer includes several motif databases that are used to help annotate
results and conduct searches for known motifs. HOMER contains a custom motif
database based on independent analysis of mostly ChIP-Seq data sets which is
heavily utilized in the software." See http://homer.salk.edu/homer/motif/motifDatabase.html
for more information on how these files were generated, and Homer's sources.
MotifDb object of length 247; to access metadata
use mcols(homer)
providerName
Name provided HOMER
providerId
Factor Name provided by HOMER
dataSource
"HOMER"
geneSymbol
Symbol provided by HOMER
geneId
Entrez gene id for the transcription factor
geneIdType
"ENTREZ"
proteinId
UNIPROT id for the transcription factor
proteinIdType
"UNIPROT"
organism
"Hsapiens"
sequenceCount
NA
bindingSequence
Consensus sequence for the motif
bindingDomain
DBD provided by HOMER
tfFamily
NA
experimentType
The Celltype, IP, Assay, and GEO id if applicable for the motif
pubmedID
"20513432" see Source for more details
Source
Heinz S, Benner C, Spann N, Bertolino E et al. (2010 May 28) Simple Combinations
of Lineage-Determining Transcription Factors Prime cis-Regulatory
Elements Required for Macrophage and B Cell Identities. Mol Cell, 38(4):576-589.
PMID: 20513432