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cytoscape / cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js
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circRNA-miRNA-mRNA (and Proteins) interaction protocol #10

Open AlexanderPico opened 6 years ago

AlexanderPico commented 6 years ago

[Franzi]

ShahnazShefa commented 6 years ago

Trying to check which pathways candidate miRNAs and groups of miRNAs are engaged in and the track down the mRNA targets. It's not working. When I did the same is geneid did work though. Any advice will be highly appreciated .

susancoort commented 6 years ago

Dear Shahnaz, Just that I understand your question correctly. Do you start with a list of microRNAs? If so how are they annotated? Are you using a Cytoscape app to find the mRNA targets? With the CyTargetLinker app you can find the predicted and/or validated microRNA target genes. Thereafter you can find the pathways in which the target genes are present. Both microRNAs-targets and target-pathway interactions can be visualized in one network. Is this what you are looking for? With kind regards, Susan Coort

From: ShahnazShefa [mailto:notifications@github.com] Sent: dinsdag 3 april 2018 16:29 To: cytoscape/cytoscape-tutorials Cc: Subscribed Subject: Re: [cytoscape/cytoscape-tutorials] circRNA-miRNA-mRNA (and Proteins) interaction protocol (#10)

Trying to check which pathways candidate miRNAs and groups of miRNAs are engaged in and the track down the mRNA targets. It's not working. When I did the same is geneid did work though. Any advice will be highly appreciated .

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ShahnazShefa commented 6 years ago

Dear Susan I do have a list of miRNA in excel . I got the acession and ID form mirbase. I did import the file to Cytscape3.6.0. I am attaching what I did in a word doc. Would be very kind of you indeed if you could advise me what I am doing wrong. Thanks Shahnaz EXAMPLE.docx

EXAMPLE.xlsx