Hello,
I am trying to determine if there are specific motifs enriched in the 3' UTRs of increased and decreased genes resulting from an RNA-Seq experiment. I extracted the 3' UTR sequences of these genes from UCSC and submitted them to AME. I also used the sequences to get Markov background models for each group (increased and decreased), respectively. I provided AME with a list of 10 motifs. When I run the program, I see that most of the motifs are highly enriched in both groups with crazy p-values. Although, the decreased genes have higher corrected p-values than the increased genes. Can someone help me interpret these data? Can I make any statement on whether a motif is
more or
less enriched in the increased genes than the decreased genes?
Thanks in advance for you help!
Example:
Increased genes: 2. Ranksum p-values of motif CPE (TTTTAT) top 1334 seqs (left,right,twotailed): 1 2.179e-63 4.359e-63 U-value: 5.562e+05 (Corrected p-values: 1 1.308e-62 1.308e-62)
Decreased genes: 6. Ranksum p-values of motif CPE (TTTTAT) top 982 seqs (left,right,twotailed): 1 1.529e-21 3.058e-21 U-value: 7.016e+05 (Corrected p-values: 1 9.173e-21 9.173e-21)