visualing pwm motif on a DNAstring
1
0
Entering edit mode
@sekawaiwai2006-9531
Last seen 7.7 years ago

Hi everyone, 

so i have been doing analysis on promoters , SL_promoter_stringset is a list of 1600 promters stringsets, MotifList are a list of pfm for around 100 motifs, namely

'M0006_1.02 ' etc

i am going to see if these motifs are part of the promoters

here is my code

dllm4<-makePriors(SL_promoter_stringset,1) 

dllm5<-toPWM(MotifList,prior = dllm4)

dllm6<-makeBackground(dllm5,bg.seq=SL_promoter_stringset,type = 'logn',bg.len = 100, bg.source = 'all at promoters split into 100bp chunks')

dllm7<-motifEnrichment(sequence = SL_promoter_stringset, pwms = dllm6)

i tried to get the background and did the motifenrichment analysis, so the outcome looks something like this  for 

dllm7$pwms$M0006_1.02

dllm7$pwms$M0006_1.02
An object of class 'PWM'
ID: M0006_1.02
Target name: M0006_1.02
Frequency matrix:
$pfm
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
A   25   14   38    0    0   20   16   35   25    18
C   39   72    0   80   96    1   68   35   16    24
G   27   13   61   19    0   71    8   16   43    17
T    9    1    0    2    4    8    8   14   16    41
Position weight matrix (PWM):
$pwm
        [,1]        [,2]        [,3]       [,4]      [,5]       [,6]       [,7]        [,8]       [,9]      [,10]
A -0.5462997 -1.36650370  0.06497302 -6.6724253 -6.658211 -0.8630223 -1.1784698 -0.06684512 -0.5462997 -1.0121416
C  1.5401439  2.42241378 -6.64385619  2.5599365  2.836785 -3.5697404  2.3401083  1.38458592  0.2617849  0.8427707
G  1.0118105 -0.03502867  2.19806183  0.4936162 -6.658211  2.4022734 -0.7263503  0.26178490  1.6805495  0.3485468
T -1.9836158 -4.76039493 -6.64385619 -3.9824608 -3.084600 -2.1464966 -2.1464966 -1.36650370 -1.1784698  0.1592327
With background nucleotide frequencies which also serve as pseudo-count:
$prior.params
        A         C         G         T
0.3667722 0.1332278 0.1332278 0.3667722 

i am wondering if there are any packages or any functions in bioconductor so that i can do further investigation in these motifs and mainly to  visually analyse if these motifs are actually exist in these promoters (i already have a list of promoters as dnastringset) and how they interact with transcription factors. thank you very much

 

 

pwmenrich dnastringset • 1.7k views
ADD COMMENT
1
Entering edit mode

You may want to try motifStack or others listed or others listed under 'visualization' in biocViews.

Valerie

ADD REPLY
1
Entering edit mode
@robert-stojnic-6136
Last seen 8.0 years ago
United Kingdom

There are functions in PWMEnrich for this, specifically motifScores() and plotMotifScores(). For me see Use case 2 in the PWMEnrich vignette:

 

http://bioconductor.org/packages/release/bioc/vignettes/PWMEnrich/inst/doc/PWMEnrich.pdf

 

Cheers, Robert

ADD COMMENT
0
Entering edit mode

thank you very much for the response, but what i really what to do is plotting these motif on the promoters ( so plotting both the promoter sequence with the motif) because i am interested to see may be just one bp change that exist in these motifs, so i guess the real question is how to plot motif as PWMs on a sequence object (may be as a biostring) with basepair showing.

ADD REPLY

Login before adding your answer.

Traffic: 755 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6