Entering edit mode
6.0 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
"I have a list of differentially expressed genes" - genes or miRNAs ?
it is miRNA.and I want to know the target genes of these miRNAs.
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
only Cumulative weighted context++ score and total context++ score is present in targetscan result.so what can I do?
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.
Sorry that answer was for miRanda output. For targetscan you can select the ones which have low total context++ scores.
KK
thank you for your reply.