associateTranscriptionFactors: associateTranscriptionFactors

In PriceLab/MotifDb: An Annotated Collection of Protein-DNA Binding Sequence Motifs

associateTranscriptionFactors

Description

In the analysis of, or exploration of gene regulatory networks, one often creates a data.frame of possible genomic regulatory sites, genomic locations where a TF binding motif matches some DNA sequence. A common next step is to associate each of these motifs with its related transcription factor/s. We provide two sources for those relationships. When you specify the "MotifDb" source, we return the motif/TF relationships provided by each of the constituent public MotifDb sources. When you specify the "TFClass" source, transcription factor family memberships (described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383905/) are - sometimes expansively - provided for each motif you supply.

This method uses, and therefore expects, different columns of the incoming data.frame to be used with each method. The MotifDb source uses the "motifName" column of the incoming data.frame. The TFClass source expects a "shortName" column in the incoming database.

A new column, "geneSymbol", is added to the incoming data.frame. This new column identifies the transcription factor associated with the motif for each row in the data.frame.

Usage

## S4 method for signature 'MotifList'
associateTranscriptionFactors(object, tbl.withMotifs, source, expand.rows, motifColumnName="motifName")

Arguments

object	a MotifList object.
tbl.withMotifs	a data.frame
source	a character string, either "MotifDb" or "TFClass" (case insensitive)
expand.rows	a logical value, recommended especially for the TFClass source, in which sometimes many TFs are mapped to the same motif
motifColumnName	a character string identifying the column in tbl.withMotifs which contains the motifs to be associated with transcription factors

Value

A data.frame with one column ("geneSymbol") and possibly multiple rows added

Author(s)

Paul Shannon

See Also

MotifDb, geneToMotif, motifToGene, subset, query

Examples

  tbl.tfClassExample <- data.frame(motifName=c("MA0006.1", "MA0042.2", "MA0043.2"),
                                   chrom=c("chr1", "chr1", "chr1"),
                                   start=c(1000005, 1000085, 1000105),
                                   start=c(1000013, 1000092, 1000123),
                                   score=c(0.85, 0.92, 0.98),
                                   stringsAsFactors=FALSE)
      # here we illustrate how to add a column with the required name:
  tbl.tfClassExample$shortMotif <- tbl.tfClassExample$motifName
  tbl.out <- associateTranscriptionFactors(MotifDb, tbl.tfClassExample, source="TFClass",
                                           expand.rows=TRUE)
  dim(tbl.out)   #    MANY tfs mapped, mostly FOX family genes
  tbl.motifDbExample <- data.frame(motifName=c("Mmusculus-jaspar2016-Ahr::Arnt-MA0006.1",
                                               "Hsapiens-jaspar2016-FOXI1-MA0042.2",
                                               "Hsapiens-jaspar2016-HLF-MA0043.2"),
                                    chrom=c("chr1", "chr1", "chr1"),
                                    start=c(1000005, 1000085, 1000105),
                                    start=c(1000013, 1000092, 1000123),
                                    score=c(0.85, 0.92, 0.98),
                                    stringsAsFactors=FALSE)

   tbl.out <- associateTranscriptionFactors(MotifDb, tbl.motifDbExample, source="MotifDb",
                                            expand.rows=TRUE)
   dim(tbl.out)   # one new column ("geneSymbol"), no new rows

PriceLab/MotifDb documentation built on March 23, 2022, 7:42 p.m.