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!
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.