Question: % Of Motif In Background--Homer Motif
0
gravatar for GeneInfo
5.9 years ago by
GeneInfo20
Canada
GeneInfo20 wrote:

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!

motif • 2.5k views
ADD COMMENTlink modified 5.9 years ago by Tky990 • written 5.9 years ago by GeneInfo20
0
gravatar for Tky
5.9 years ago by
Tky990
Japan
Tky990 wrote:

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.

ADD COMMENTlink written 5.9 years ago by Tky990

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.

ADD REPLYlink written 2.4 years ago by sophialovechan30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1639 users visited in the last hour