Question: MEME result v FIMO result for target annotation
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gravatar for YaGalbi
2.5 years ago by
YaGalbi1.5k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.5k wrote:

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
annotation meme fimo • 1.1k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by YaGalbi1.5k

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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Santosh Anand5.1k

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

ADD REPLYlink written 2.5 years ago by YaGalbi1.5k

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

ADD REPLYlink written 2.5 years ago by Santosh Anand5.1k
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