How to extract information from RNA-seq data?

Question

[Newcomer]

Hi everyone I'm new to the fields of systems biology and bioinformatics. I have been given TEXT files of miRNA and mRNA sequencing data including library size and read counts per sample for a cohort of patients and healthy controls. I have done differential expression analysis for both files using edgeR and now wonder what other software/packages/etc. I can use to get more information from this data. Any suggestion is highly appreciated.

Answer 1

[k.kathirvel93]

Since you have done DE Analaysis, now you have some list of miRNAs and mRNAs. So,

Perform target gene prediction for DEmiRNAs and correlate them with the DEmRNAs from mRNA-seq. Downregulated miRNA's target gene should be upregulated in mRNA-seq .

Then perform Pathway analysis for DEmRNAs from mRNA-seq, and find any disease associated pathways are dysregulated or not.

Finally, validate the expression of miRNA and mRNA in qRT-PCR, by different conditions, like knockout of DE genes, miRNA-mimic or inhibitor, etc.

[Newcomer]

Thank you for your response. I'm now wondering what tools I can use to do correlation analysis. Could you please advise?

[k.kathirvel93]

Yes.

1. I prefer miRwalk V3 for miRNA human target prediction with filter of considering only >.9 score targets with validation. Target gene prediction is really very important, so try to comeup with best hits.

2. Then, manually check the correlation, like The upregulated miRNA's binding target gene should be get downregulated in mRNA-seq. and look reverse too.