Question: Issue with replicating from a research paper-motifs
0
gravatar for joshua.steier
17 days ago by
joshua.steier20 wrote:

Greetings, I've been trying to replicate results from the following research article: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2378-9 In the paper, there is a figure that describes motif #57 with a sequence logo and its position weight matrix.

I took the data from the given datasets in additional material section and gathered the FASTA files needed to process through MEME.

The combined dataset(denoted CM in the paper) was processed through MEME but I obtained different motifs than those obtained by the authors. I checked the datasets and my FASTA files and they are correct, I'm unsure of how this discrepancy between my results and theirs exists, as I followed the paper.

I suspect that maybe the FASTA files changed over a year in the Uniprot database since the paper is from 2018 and we are in 2019. I searched in MEME for motifs with length 3 to 10, as this describes the motifs discussed in the paper.

Any thoughts or possible directions?

Here is the Motif they are showing: (57) motiftheygot

Here is the motif I got:

motifIgot

motif sequence meme rna fasta • 211 views
ADD COMMENTlink modified 16 days ago by geek_y9.6k • written 17 days ago by joshua.steier20

Have you checked whether you're using the same MAST/MEME versions? I've seen quite a bit of discrepancy there

ADD REPLYlink written 17 days ago by Philipp Bayer6.0k

You're correct to address that, I believe our MEME versions are different. The one I'm using is 5.0.5 and the one they used is most likely 5.0.0. Would the difference in version cause this much of a difference?

ADD REPLYlink written 17 days ago by joshua.steier20

I've had some large differences in the past, but with earlier versions than that - have you tried rerunning with MAST/MEME 5.0.0 from http://meme-suite.org/meme-software/5.0.0/meme_5.0.0.tar.gz ?

ADD REPLYlink written 16 days ago by Philipp Bayer6.0k
1

Hi, I just ran MEME under that version for the motifs and got the same results as I got before.

ADD REPLYlink written 16 days ago by joshua.steier20

Thanks for checking :)

ADD REPLYlink written 15 days ago by Philipp Bayer6.0k

Thank you for your help :)

ADD REPLYlink written 15 days ago by joshua.steier20

Update: I found out the authors are using MEME version 4.10.1. Do you think this likely caused the discrepancy? I'd like to test it out but I'm having some difficulty getting 4.10.1 to work on linux server.

ADD REPLYlink written 3 days ago by joshua.steier20

Interesting! Conda has 4.11 and 4.8, maybe try those?

https://bioconda.github.io/recipes/meme/README.html

You can either install the version as a Docker image:

docker pull quay.io/biocontainers/meme:4.11.1-0

or via conda:

conda install meme=4.11.1-0

replace 4.11.1-0 by 4.8.1-1 to see the really old meme - if you see the same results as yours' in 4.11 and 4.8 I'd doubt they appear in 4.10

ADD REPLYlink written 2 days ago by Philipp Bayer6.0k
1

Thanks! Using Conda was much better than the standard methods. I ran it on 4.11 and 4.8, the authors' results showed on both of those. So the version must be causing the discrepancy as you said. I'm going to try to replicate given the now correct motifs from the old version. Do you suppose it is also worthwhile to replicate their methods using the new motifs from the newest MEME version?

ADD REPLYlink written 1 day ago by joshua.steier20

Interesting!! Good to know that you got the old result :) If the motifs are so different, which one is the 'correct' version then? I presume their results will not hold up using the newest MEME version, or you'll get completely different results..

ADD REPLYlink written 1 day ago by Philipp Bayer6.0k

Can you elaborate/show which motif they are showing and which motif you got ?

ADD REPLYlink written 17 days ago by geek_y9.6k

Here is the Motif they are showing: (57) motiftheygot

Here is the motif I got:

motifIgot

ADD REPLYlink modified 16 days ago by geek_y9.6k • written 17 days ago by joshua.steier20

Thanks. I added it to the question. Looks like a huge difference. Did you check all our motifs ? May be not the top motif but the motif authors showed might be somewhere on the list. If not, I would directly contact authors.

ADD REPLYlink written 16 days ago by geek_y9.6k

Thanks for adding it to the question, your help is greatly appreciated. I looked at my results again and couldn't find that motif. I'll try contacting the authors, I appreciate your suggestions.

ADD REPLYlink written 16 days ago by joshua.steier20
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