lncRNA transcript databases for RNA-Seq analysis

[mortonm33]

Hello all,

I'm wondering if anyone has experience with or has seen a comparison of the various transcript databases (RefSeq, Ensembl, UCSC) for analyzing RNA-Seq data with respect to lncRNAs. It seems that there are many more transcripts present in some of these databases than in others and I was hoping someone might be able to provide some explanation or guidance as to which would be best for studying differential expression of lncRNAs. Thanks in advance for any responses.

M

[Milan Radovich]

I use the lincRNA database in UCSC. You can download using their table browser.

[mortonm33]

Hi Milan,

Thanks for the response. I'm interested to know if you have tried other databases and if you can comment on how they compare or how you went about selecting the appropriate database.

Thanks,

Matt

[Milan Radovich]

No, unfortunately have not tried any other database.

[rnaNGS]

ChIPBase uses lncRNAs (lincRNAs) that fetched and filtered from Ensembl, refSeq, UCSC databases and literatures (Cabili et al. 2011, Genes Dev., 25, 1915-1927; Guttman et al. 2010, Nat Biotechnol, 28, 503-510; Belgard et al. 2011, Neuron, 71, 605-616. Young et al. 2012, Genome Biol Evol, 4, 427-442.). You can download them from ChIPBase database .