target gene selection for miRNA
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3.8 years ago
anjuraas ▴ 10

hi I have a list of differentially expressed genes. i used targetscan for finding the target genes. As I have to work on miRNA: mRNA interaction in gastric cancer I have to select target genes related to that. How can I narrow down my target genes? thank you

miRNA target genes • 1.2k views
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"I have a list of differentially expressed genes" - genes or miRNAs ?

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it is miRNA.and I want to know the target genes of these miRNAs.

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Hi,

You can filter the targetscan results by selecting the ones having energy threshold less than -20 Kcal/mol. Also check the percentage coverage of your query and you can filter based upon them too.

KK

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only Cumulative weighted context++ score and total context++ score is present in targetscan result.so what can I do?

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If you have list of differentially expressed mRNA from the same sets of samples, it will be easier to narrow down your target genes based on their opposite expression patterns.

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Sorry that answer was for miRanda output. For targetscan you can select the ones which have low total context++ scores.

KK

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thank you for your reply.

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