non-coding RNAs target predictions

Question

[Leite]

Hello everyone,

I have a list with some non-coding RNAs related with one disease, so I would to look for interactions between this ncRNAs and mRNA. Well, to miRNA I found a lot of databases for target predictions, but for others ncRNA I cant found.

My list is composed for:

Long intergenic non-protein coding RNAs (LincRNA) = 11 Non-coding RNAs (ncRNA) = 7 Small nucleolar RNAs (snoRNA) = 2

Anyone know a database or a way to predict targes for this ncRNAs?

Best regards,

[Kevin Blighe]

Dear Leite,

These may be of help in achieving your goals:

• RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins
• Using RNA secondary structures to guide sequence motif finding towards single-stranded regions

[Asaf]

Are you certain about the mechanism being direct interactions with mRNAs?

[Leite]

Dear @Asaf

Yes, I'm certain about the miRNAs but not about the others ncRNAS, this can interact with others genetics elements?

There is one tool to do that?

Best regards,

Answer 1

[lsp03yjh]

You may use lncRNA-target interactions ( http://starbase.sysu.edu.cn/rnaRNA.php?source=lncRNA ) and small ncRNA-target interactions ( http://starbase.sysu.edu.cn/rnaRNA.php?source=sncRNA ) supported by LIGR, PARIS, SPLASH and MIRAO that are high-throughput RNA interactome sequencing data.