Understanding output about mixmir

[ldiao]

Hi Bharata,

MixMir does not return a list of genes that the miRNA binds to: it searches
over all possible motifs and finds ones which are highly associated with
changes in gene expression values, and thus are more likely to belong to
active miRNAs. Thus, any gene whose UTR contains the motif is more likely
to be targeted.

Hope that helps,
Liyang

On Thu, Mar 3, 2016 at 12:58 AM, Bharata kalbuaji [email protected]
wrote:

Hello,
I got the result and I have a question. So, from this program, I can get
the miRNA which is predicted to bind the mRNA based on the log fold change
of genes. The output file is a CSV file of miRNA matched to a motif with
p-value ranked from the lowest to a certain number of rank. Is it possible
to know what gene are those miRNA bind to? All I can get is the rank,
motif, p-value, coef, NUTRs, and miRNA matched. I want to know what gene
paired with what miRNA. I attached my result file. Thank you.
BDC_647-MixMir-results.txt
https://github.com/ldiao/MixMir/files/156229/BDC_647-MixMir-results.txt

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#2.

[18209018]

Thank you Liyang for your reply.

Another question about the search of the motifs. The input is FASTA for the 3'UTR for the gene and the miRNA. I imagine it searches by "aligning" the miRNA sequences to the 3'UTR sequences right? Probably I can modify the code to inform me the gene which miRNA motifs sequences is found. I imagine the result would be a pair of miRNA and gene name. How do you think?

[ldiao]

Hi Bharata,

Yes, you can certainly do a search for all genes which contain the motifs
of interest (the column NUTRs tells you how many such genes exist in your
data). In that case, you can obtain a list of miRNA-gene pairs as desired,
and maybe sort by those genes with greatest change in expression.

Best,
Liyang

On Thu, Mar 3, 2016 at 2:32 PM, Bharata kalbuaji [email protected]
wrote:

Thank you Liyang for your reply.

Another question about the search of the motifs. The input is FASTA for
the 3'UTR for the gene and the miRNA. I imagine it searches by "aligning"
the miRNA sequences to the 3'UTR sequences right? Probably I can modify the
code to inform me the gene which miRNA motifs sequences is found. I imagine
the result would be a pair of miRNA and gene name. How do you think?

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#2 (comment).