Finding Transcriptional Factor Binding Motifs by Table Browser in UCSC

Question

[mitaminmog]

I want to find how many motifs bind to the Transcription Factor of ANO1 gene. Would you please help me how to use Table Browser to find Transcriptional Factor binding motifs for gene?

Thank you very much.

Answer 1

[Alex Reynolds]

To my knowledge, the UCSC browser does not offer tables with transcription factor binding sites.

You could make a set of binding sites with FIMO, the JASPAR MEME or other MEME database files available via the MEME download site, and your genome build of interest (per-chromosome FASTA files from UCSC goldenpath, say), e.g. for hg19:

$ for chr in `seq 1 22` X Y; do echo $chr; wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/chr$chr.fa.gz | gunzip -c - > hg19.chr$chr.fa; done

The output of a FIMO search includes a GFF file you can convert to BED via gff2bed.

Once you have a sorted BED file of binding sites from gff2bed, you can use bedmap --echo-map or similar to locate and count the number of binding sites which overlap annotations that associate with the ANO1 HGNC description. To get HGNC descriptions and their locations, e.g. for hg19:

$ wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz | gunzip -c | awk -v OFS="\t" '($$9>1){ print $$3,$$5,$$6,$$13,$$9,$$4 }' | sort-bed - > hg19.hgnc.bed

Filter for ANO1 regions:

$ awk '$4=="ANO1"' hg19.hgnc.bed > hg19.hgnc.ANO1.bed

Then, for example:

$ bedmap --echo --echo-map-id-uniq hg19.hgnc.ANO1.bed hg19.jaspar_fimo.bed > answer.bed

To count the number of unique JASPAR motif models that overlap the ANO1 space, for example:

$ wc -l answer.bed