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

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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 • 727 views

ADD COMMENT • link 2.8 years ago by diego1530 ▴ 80

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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

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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

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