visualing pwm motif on a DNAstring
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Entering edit mode
@sekawaiwai2006-9531
Last seen 5.5 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 • 1.0k views
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You may want to try motifStack or others listed or others listed under 'visualization' in biocViews.

Valerie

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@robert-stojnic-6136
Last seen 5.9 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

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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.