A recent approach to identify lncRNAs from a large list of differentially expressed genes

0

Entering edit mode

2.8 years ago

diego1530 ▴ 80

I trust everyone is doing well.

From RNA-seq data analysis of adenocarcinoma samples with the GTF annotation of ensembl's GCh38, I obtained the raw quantification using RSEM. Subsequently, I used edgeR to perform differential expression analysis by comparing my adenocarcinoma vs. control samples. As a statistical design, those genes and lncRNAs with a lfc > 2 and a p-value < 0.05 by BH method were considered differentially expressed.

I currently hold a large list which includes genes and lncRNAs differentially expressed and as a main task, I need to identify from this list, which ones correspond to lncRNAs and mRNAs. Perhaps anyone could provide me a hint of a program or method to strictly distinguish lncRNAs from mRNAs in order to identify them from this list?

Thanks in advance!

RNA-seq edgeR lncRNAs mRNAs • 724 views

ADD COMMENT • link 2.8 years ago by diego1530 ▴ 80

0

Entering edit mode

Can you clarify what the problem is? The gene biotype is annotated in the Ensembl GTF so you can simply look it up. Where do you get stuck?

ADD REPLY • link 2.8 years ago by ATpoint 85k

0

Entering edit mode

If I got a list of differentially expressed genes, how can I identify lncRNAs that are differentially expressed?

ADD REPLY • link 2.8 years ago by diego1530 ▴ 80

Login before adding your answer.