Question: can TissueEnrich be used to calculate the tissue-specific lncRNAs in plants?
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gravatar for Carina Yang
3 months ago by
Carina Yang0 wrote:

TissueEnrich is a wonderful tool for the identification of tissue-specific protein coding genes. I am wondering whether it is suitble for calculating the tissue-specific lncRNAs as well. Generally, the expression of lncRNA is rather lower than protein coding gene. Maybe Genes with an expression level greater than or equal to 0.1 (TPM or FPKM) is more reasonable.

tissueenrich • 77 views
ADD COMMENTlink modified 3 months ago by Ashish Jain0 • written 3 months ago by Carina Yang0
Answer: can TissueEnrich be used to calculate the tissue-specific lncRNAs in plants?
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gravatar for Ashish Jain
3 months ago by
Iowa State University
Ashish Jain0 wrote:

Hi Carina,

Thank you for your interest in our tool. As you know, we only have data protein coding genes data and it doesn't have information about the lncRNAs. However, if you want to explore more about the tissue-specific lncRNAs and you have the lncRNAs data from different tissues, you can always use the teGeneRetrieval function to get tissue-specific lncRNAs and change the different parameters according to your use case like foldChangeThreshold, expressedGeneThreshold, and maxNumberOfTissues. I hope I answered your question. Feel free to ask any other questions or concerns.

Regards, Ashish Jain

ADD COMMENTlink written 3 months ago by Ashish Jain0

Many thanks! I will have a try later.

ADD REPLYlink written 3 months ago by Carina Yang0
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