MEME result v FIMO result for target annotation

Question

[BioinfGuru]

Hi all,

For simplicity I have a single sample that I have run meme-chip on. Also, for simplicity lets assume there is a single motif returned as enriched. The output of the single meme-chip run includes meme results and fimo results. I want to:

1) Identify the genomic locations of all occurances of the enriched motif.

2) Choose an appropriate q-value cut-off for annotation of target genes.

Meme (which looks for enriched motifs) has constructed a PWM of the enriched motif from 5 sequences (q-value <= 0.001). The PWM includes any variable positions within the 5 sequences. This PWM is used as the input to Fimo (which identifies all occurances of the PWM). Fimo returns 10 sequences that match the PWM (q-value <= 0.001).

What has me confused is that 7 of the 10 sequences from Fimo match exactly the 5 sequences from Meme.

So why did meme fail to find those extra 2 that fimo found?

Thank you all

Kenneth

NOTE:  - capitalisation is just to highlight variation
       - each sequence has its own coordinates (chr/start/end columns not include here)


MEME RESULT
cgtagcta
cgtagcta
Agtagcta
cgtaActa
cgtaActa

PWM (constructed from the 5 sequences)
WgtaPcta     # where P can be a or g, and W can be a or c

FIMO RESULT
cgtagcta           # matches the PWM + 1 of the 5 meme sequences exactly
cgtagcta           # matches the PWM + 1 of the 5 meme sequences exactly
Agtagcta           # matches the PWM + 1 of the 5 meme sequences exactly
cgtaActa           # matches the PWM + 1 of the 5 meme sequences exactly
cgtaActa           # matches the PWM + 1 of the 5 meme sequences exactly
AgtaActa           # matches the PWM only
AgtaActa           # matches the PWM only
AgtaActa           # matches the PWM only
cgtagcta           # matches the PWM + 1 of the 5 meme sequences exactly
agtagcta           # matches the PWM + 1 of the 5 meme sequences exactly

[Santosh Anand]

Probably I'm missing something, but

Agtagcta           # matches the PWM + 1 of the 5 meme sequences exactly
and
AgtAgcta           # matches the PWM only

are the same. They match both the PWM and sequences. There is only the difference of CAPITALIZATION of one of the inner A

[BioinfGuru]

edited...that was a typo...thx

[Santosh Anand]

What happens if you increase the p-value threshold of meme from 0.001?