% Of Motif In Background--Homer Motif

Question

[GeneInfo]

I just get some result from HOMER using findMotifsGenome.pl All the parameters are in default and -mask option is used. From this histone-Ab ChIP-seq data, motif ranking NO.1 occur in 38% of targets, but meanwhile it occurs in 30% of the background. I read some paper and found people often do not show the percentage of background for the motif. Is there any guideline to tell how significant the result is? 38% Vs 30% is not that convincing to me. Any suggestion is appreciated!

Answer 1

[Tky]

The significance can be judged by enrichment P- value. As stated in the Homer homepage: "In general, when analyzing ChIP-Seq / ChIP-Chip peaks you should expect to see strong enrichment for a motif resembling the site recognized by the DNA binding domain of the factor you are studying. Enrichment p-values reported by HOMER should be very very significant (i.e. << 1e-50)"

Thus usually only P-value and percentage in targets are reported.

[sophialovechan]

Hi, I have done findMofifsGenome.pl for my data. But the p-values in the results are very high (0.00001-1, most of them are at 0.01). What would be the possible problems and are there any other analysis that I can use under my situation?

I used the same scripts to run some other data and the results are good, though.