Hi,
I just wondering if any good platform and protocol for downstream analyses of long non-coding RNAs (lncRNAs) in livestock species, with novel lncRNAs obtained from sequencing data.
I went through 40 tools and databases listed in the Omictools.com, but could not find the suitable one. The http://www.noncode.org is good but supported only the know lncRNAs.
I also looking for any R-package or worklows which can support the annotation of lncRNAs to biological processes (GO) or pathways.Given that we only knew the positions and sequences of lncRNAs
Any suggestions are welcome.
Thanks
There are various databases for linkRNAs, you may want to go through this list and see which one is suitable for your experiment/species.
https://en.wikipedia.org/wiki/List_of_long_non-coding_RNA_databases
Since most lncRNAs are not annotated, we can annotate them via correlation with protein coding genes. Check the method described in this paper:
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
https://www.ncbi.nlm.nih.gov/pubmed/22110045
hi
take a time to look at this paper, I'm sure it will help you in your analysis:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0570-4
Thank you for all suggestions, I found different ways to infer the lncRNAs functions (cis and trans regulation), either by their position, correlation with mRNAs, co-expression with mRNAs or miRNAs or weighted expression networks, their results make sense somehow but not completely convinced.
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