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4.0 years ago
mathavanbioinfo
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Hello All I want to do the enrichment analysis for list of lncRNAs (500 lncRNA), is there any tool or methods available for doing it.
Hi,
I'm not sure if you can do it. Perhaps I'm wrong, but as far I understand gene enrichment analysis involves the search of enriched pathways/ontologies based on some interesting gene list - from differentially expressed genes. Since you have long non-coding RNA genes, these are non-coding genes, even if they play some role, I think they do not have pathway/ontologies associated, but I'm not 100% sure.
Just curiosity, did you see any enrichment analysis for lncRNA described online or in any paper? If so, can you put that references here. I would like to check them.
António
https://www.nature.com/articles/srep34161
Thank you for the paper. I still maintain my opinion, but perhaps someone with more experience may want to comment further.
So, accordingly to their material and methods section Functional classification and pathway analysis what I think they did was, they first found the co-expression between lncRNA and mRNAs based on correlation analysis resulting in what they called lncRNA co-expressed mRNA. Then, I think, but I'm not sure, that for the lncRNA of interest, they search the respective co-expressed mRNA and, only then, they performed GO enrichment analysis for these mRNA (which have function and are involved in pathways). Since they assume a relationship between these lncRNA co-expressed mRNA, they called lncRNA GO enrichment. This is my interpretation, but I did not read the full paper, only that section of methods.
Anyway, you can try to reach the authors of that paper asking which tool they used and how they did it.
António
lncRNAs are functionally involved in serval biological processes. However, they are not represented in any databases like KEGG or GO BP. Mainly because lncRNAs exert their functions by targeting protein coding genes, located nearby or far. Recently, there are a couple of databases that have reported certain lncRNAs and their association with cancer hallmarks. LncSEA, for example. http://www.bio-bigdata.net/lnc2cancer/index.html >lnc2cancer
LncRNAs are very dynamic. It has more cell type and tissue specific temporal expression unlike stable expression of protein coding genes. Hence lncRNAs are involved in diverse function depending on the cell or tissue type you are working with. It will be hard to generalize functions for lncRNAs. In your case you can try either of these (But this is not the gold standard, just approximation of your conclusions. you always need to validate it experimentally),
1) Find protein coding gene with co-expression analysis (since lncRNAs are know to have coordinated functions with protein-coding genes)
2) Proximity analysis by considering protein coding genes near to the lncRNAs of interest (since lncRNAs are also cis regulators for the near by protein coding genes). It will be hard to find the trans genes without specific experimental setup.
You can use either of these approaches to extract related PCGs and find the related pathways or ontologies.