Hi all,
I have a data-set from TCGA consisting of miRNA and mRNA (example files attached). I would like to find the interaction between these two datasets, as in the up-regulation and down-regulation of genes, specifically I am looking at mir34-b. Further, I would also want to know the interaction of miRNA and mRNA in the complete data-set (The attached files are just one among the approx. 200 sample files).
Is spearman correlation a good measure to start with? Also, could some of you give a brief idea on how to approach this?
I also apologize for any mistakes as I am new to this topic! Thank you all for your help and response and I hope the question is clear.
Well this is really a "big" question, you can refer to this paper : Joint analysis of miRNA and mRNA expression data. Good luck.
Maybe first have a look on http://cancerminer.org and the related paper
Jacobsen A, Silber J, Harinath G, Huse JT, Schultz N, Sander C: Analysis of microRNA-target interactions across diverse cancer types. Nat Struct Mol Biol 2013(October):1–9. http://www.ncbi.nlm.nih.gov/pubmed/24096364
They used a combination of microRNA target predictions and a rank-based statistical score, but there is probably a way to make it better and to validate such large scale predictions.
Good luck
A complementary approach could be looking for relations based on the expression profiles of both kinds of data together, as proposed in https://www.ncbi.nlm.nih.gov/pubmed/25883093.
Using both approaches you got the relations from the previous knowledge and the interactions from your own dataset.
We could help performing the analysis if needed.
Best
Angelo
https://www.ncbi.nlm.nih.gov/pubmed/25883093
Dear Anuroop,
Integrative analysis of quantitative mRNA expression profiles with miRNA target predictions relies on the detection of significant negative correlations between the fold changes of the two putatively interacting RNAs. I have reviewed this in detail in the article ‘Principles of miRNA–mRNA interactions: beyond sequence’ (available here at RG).
Regarding miR-34b as your miRNA of interest, there are several databases available that provide a list of putative and/or experimentally validated target mRNAs (miRTarBase, TarBase, miRecords, miRNAMap, TargetScanS, microRNA.org, miRDB, miRGator, PicTar, RNA22, DIANA, MicroInspector, miRo).
Most of these databases contain different entries for a given miRNA, and therefore it’s best to use an overlapping set of target genes that contains either experimentally validated targets or only those, which were predicted by several different algorithms/databases.
‘omiRas: A webserver for the interactive analysis of paired small RNA-Seq experiments’ (also available here at RG) is a web-based tool that allows you to upload sequencing data from small RNA experiments along with a list of differentially expressed mRNAs to check for significant negative correlations of putatively interacting miRNAs and mRNAs. The tool permits to choose any combination of target predictions from 8 implemented and publicly available databases.
The only problem is that omiRas requires the raw sequencing data for miRNAs, and not the expression matrix that you uploaded as an example. A matrix works for mRNAs though. If you can also extract the original miRNA sequencing data from TCGA, I srrongly recommend you to test our tool. If not, try to find something similar, which also accepts pre-processed miRNA data (in this case please let me know if you find anything).
I hope this helps. With best regards from Frankfurt,
F. Afonso-Grunz
Dear Venkateswaran,
Hi,
Good Morning. Can you please help me a procedure to download miRNA and mRNA dataset from TCGA database. or please share the downloaded dataset of 200 sample files as you said you have them. Please help me in this regard.
Regards
Mahendran
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA