homerkit
homerkit is an R package that implements functions to read HOMER output
files.
Installation
How to install HOMER: http://homer.salk.edu/homer/download.html
install.packages("devtools")
devtools::install_github("slowkow/homerkit")Usage
1. Run HOMER findMotifs.pl on your target genes
head -n3 target_genes.txt
ENSG00000003989
ENSG00000017427
ENSG00000028277gene_file="target_genes.txt"
bg_file="background_genes.txt"
out_dir="output"
mkdir -p $out_dir
# Find motifs that are enriched in the promoters of your target genes.
findMotifs.pl $gene_file human $out_dir \
-bg $bg_file &> ${out_dir}/run_homer.log2. Run HOMER annotatePeaks.pl on every motif
# Find the target genes for each motif.
for motif in $out_dir/*/*.motif; do
if [[ ! -f ${motif}.tsv ]]
then
annotatePeaks.pl tss hg38 \
-size -500,250 -m $motif -list $gene_file \
1> ${motif}.tsv 2> ${motif}.tsv.log
fi
done3. Read all of the HOMER output files with homerkit
# install.packages("devtools")
# devtools::install_github("slowkow/homerkit")
library(homerkit)
h <- read_homer_output("output")Novel motif target genes:
head(split(h$novel_motif_peaks$gene_name, h$novel_motif_peaks$motif), 3)$motif1
[1] "RERG" "CSF3" "CXCL6" "CXCL1" "CXCL5" "CXCL3" "CXCL2" "CSF2" "ELF3"
$motif10
[1] "IER3" "MT1X" "MMP3" "CCL20"
$motif11
[1] "IL6" "CCL7" "CXCL6" "CXCL1" "CXCL5" "CXCL3" "CXCL2" "GPR183"
[9] "NR4A2" "PLD1"
Possible transcription factors that match motif1:
subset(h$novel_motif_tfs, motif == "motif1")# A tibble: 10 × 8
match_name match_rank offset
<chr> <dbl> <dbl>
1 NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer 1 2
2 RELA/MA0107.1/Jaspar 2 2
3 MF0003.1_REL_class/Jaspar 3 2
4 NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer 4 1
5 REL/MA0101.1/Jaspar 5 2
6 NFKB2/MA0778.1/Jaspar 6 1
7 PB0012.1_Elf3_1/Jaspar 7 4
8 NFATC1/MA0624.1/Jaspar 8 5
9 NFATC3/MA0625.1/Jaspar 9 5
10 NFKB1/MA0105.4/Jaspar 10 1
# ... with 5 more variables: orientation <chr>, score <dbl>, motif <chr>,
# alignment1 <chr>, alignment2 <chr>
Known motif target genes:
head(split(h$known_motif_peaks$gene_name, h$known_motif_peaks$motif), 3)$known1
[1] "MAP3K8" "CFB" "CSF3" "CXCL8" "CXCL6" "CXCL1" "CXCL5" "CXCL3"
[9] "CXCL2" "NR4A2" "ELF3" "PID1"
$known10
[1] "RERG" "SPECC1L-ADORA2A" "IER3" "CFB"
[5] "SLC11A2" "NR4A1" "IL23A" "MT1L"
[9] "CXCL8" "CXCL1" "CXCL3" "CXCL2"
[13] "FLVCR2" "STEAP1" "SERPINA9" "AVPI1"
[17] "GPR183" "MMP3" "PTGS2" "ELF3"
[21] "HSD11B1" "CCL20"
$known11
[1] "CSF3" "PIM2" "MT1X" "GAB2" "SERPINA9" "IGF1"
[7] "IL1B" "TNFAIP6" "STAT4" "ELF3" "ACKR3"
Known transcription factors:
head(unique(h$known_motif_peaks[,c("motif", "best_guess")]), 3)# A tibble: 3 × 2
motif best_guess
<chr> <chr>
1 known1 NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer
2 known2 NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer
3 known3 TATA-Box(TBP)/Promoter/Homer
Contributing
Please submit an issue to report bugs or ask questions.
Please contribute bug fixes or new features with a pull request to this repository.