This function scans the promoter regions of protein-coding genes for transcription factor (TF) motifs.
It extracts promoter sequences using an Ensembl database (EnsDb) and then searches these sequences
for TF binding motifs using position frequency matrices (PFMs). The Seurat object is updated with a matrix
of motif-gene matches, a list of target genes for each TF, and additional motif information.
Arguments
- seurat_obj
A Seurat object that will be updated with motif scan results.
- pfm
A list of position frequency matrices (PFMs), such as those from the JASPAR2020 database.
- EnsDb
An Ensembl database object (e.g.,
EnsDb.Hsapiens.v86orEnsDb.Mmusculus.v79) containing gene and promoter annotations.- species_genome
A character string specifying the genome version (e.g., "hg38" for human or "mm10" for mouse).
- wgcna_name
A character string specifying the name of the WGCNA experiment to associate with the motif data (optional). If NULL, the active WGCNA experiment in
seurat_obj@miscwill be used.
Value
A modified Seurat object containing the results of the motif scan, including:
seurat_obj@misc$motif_matrix: A binary matrix indicating motif matches for each gene.seurat_obj@misc$motif_info: A data frame containing motif names, IDs, and the number of target genes.seurat_obj@misc$motif_targets: A list of genes targeted by each motif.seurat_obj@misc$pfm: The original PFMs used for the motif scan.
Details
The MotifScan function performs the following steps:
It extracts promoter regions (typically 2 kb upstream of the transcription start site) of protein-coding genes from the provided
EnsDb.It uses the
motifmatchrpackage to search these promoters for TF motifs, using the input PFMs.The function returns the Seurat object updated with several key pieces of information:
A motif-gene match matrix indicating the presence or absence of each motif in the promoter of each gene.
A list of target genes for each TF based on motif presence.
A summary of motifs, including the number of target genes for each TF.
This data is stored in the
seurat_obj's metadata and can be used for downstream analysis, such as regulatory network inference.