Non coding RNA expression data

Question

[jack]

Hi all,

I'm looking for database which contains expression levels of total RNAs.

I have tried TCGA, but it's mostly for protein coding and miRNAs.

Does anyone can help me with that?

Answer 1

[Evgeniia Golovina]

You can try GEO database.

Paste, for example, "Non coding RNA" in search field. Then, you can filter by "Non-coding RNA profiling by high throughput sequencing". Review results.

Answer 2

[EagleEye]

Check out these resources,

A: cancer genes database

In addition to those:

https://www.insilicodb.com/browse

http://www.xingene.net/ccg/download.php

Mammalian Transcriptome Database

https://bioinforx.com/lims2/blog.php?id=1000030 (Useful links)

http://medicalgenomics.org/rna_seq_atlas

http://www.brain-map.org/

[Saber HQ]

Thanks for the great list. Actually, I am interested in investigating the correlation between specific lncRNA's expression and the mRNA expression of a list of genes. So far I found MiTranscriptome and TANRIC useful. I am interested in getting both lncRNA exp and mRNA exp in similar samples (for example: TCGA normal and cancer cell samples)

The first three are not accessible but thanks again for providing these info.

[EagleEye]

Did you try Synapse TCGA project repository?

My previous similar post

Answer 3

[Charles Plessy]

Have a look at the FANTOM5 expression atlas. Expression is quantified at the level of transcription start sites, and is not restricted by a priori definitions of gene structures. Only after peak calling, the expression peaks have been associated with overlapping or neighbor gene models (GENCODE, ...).

Answer 4

[h.mon]

modENCODE has transcriptional profiles from total RNA for D. melanogaster and C. elegans.

Answer 5

[verma]

Hey Hii,

Please use ChIPBase database and also you can try to use mirCoX database. It may help to sort your problem.

Regards,
Garima Verma

Answer 6

[Saber HQ]

As for Long non-coding RNAs expression, you can try TANRIC website