Query regarding transcriptome analysis

Question

[simar-coasab]

I have whole transcriptome data from three different plant species. From Differential gene expression analysis (DGE), I got zero expression value (read count and FPKM value) for few genes in one out of three species. Is this type of result possible from whole transcriptome data?

[Benn]

I think you need to explain a bit more about your experimental set up and your methods to expect us to give you a good answer.

If you have read count per gene, and some of them have zero. Yes that is possible, if a gene is not expressed, there is no mRNA so there will be no reads.

[simar-coasab]

Thanks for your response b.nota and andrew.j.skelton73. I have whole trancriptome data, from every part of a plant. I am analysing some important genes, for e.g., genes related to flowering pathway. Some of the genes does not show any expression in any one line from three lines of a species. Is this possible from whole transcriptome data that a gene doesnot express with in lines of same species?

[Benn]

I think it is possible that some genes are expressed in some species while they are not in others. However, it's hard to say (from your info) whether it is of biological or technical cause.

I mean, what reference did you use? From only one of the species, right? And the genes that don't express in all, how similar is the sequence between the species?

[simar-coasab]

This is not from different species. This is from different varieties of a plant species.

[andrew.j.skelton73]

Just because it's a different variety of the species, doesn't mean that you won't see transcriptional differences, in fact, i'd be surprised if you didn't. I'm not sure about your experimental setup still, because you say you did a transcript assembly using trinity, but on what? - Your 3 different "varieties" of sample separately, then merged the assembly?

[andrew.j.skelton73]

What software did you use to do this analysis?

[simar-coasab]

using edgeR from Trinity

Answer 1

[andrew.j.skelton73]

To give an accurate answer, we'd need to know about the methods used to produce the transcriptome analysis you got. It is possible for some programs to call 0 for a transcript, if there are a lot of transcript variants of the gene. More information about the experiment as a whole are needed; number of reads, read length, sequencer, analysis pipeline.