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I want to identify the most highly expressed genes across several developmental stages of a given insect, in hopes of identifying a protein that can be used to design an insecticide. I have a few doubts :

  1. Several studies have been performed on individual developmental stages and their transcriptome has been published. Should I compare each set of data against the other manually, to find genes that are expressed universally and then target the most highly expressed ones or is there any software / computational method that can be used instead?

  2. Does this strategy make any sense? Is it scientifically sound? Is it right to compare transcriptomes to find commonly expressed genes?

I did try to look at the materials and methods section of a few papers on comparative transcriptomics, but it only says that data was compared, not really how it was. One paper cited VennBLAST, but I wasn't able to find the tool online.

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  • $\begingroup$ Could you clarify what do you mean by individual developmental stages? They looked at the same individual in several stages or they look in several samples different stages of development. What I think you want to do is find differentially expressed genes, search for those terms and let us know if you need something else $\endgroup$ – llrs Jan 4 '18 at 17:08
  • $\begingroup$ I mean that each paper concentrates on a single developmental stage. They analyze several samples for different stages of development. Also, no, I do not want to find differentially expressed genes.From what I understand, differentially expressed genes are those that are upregulated only in a particular cell type (in my case stage). I want to find out if a common set of genes are being upregulated throughout the life cycle of the insect, ie. they are common to all the life stages. I thought I can do this by analyzing the transcriptomes of each stage. I hope this is clear! $\endgroup$ – Cookie-san Jan 4 '18 at 17:24
  • $\begingroup$ You can find the differentially expressed genes that are downregulated too, and it is not specific to a cell type that depends on your data. But it is a comparison between two stages, so you can compare all the initial stage with all the following stages. Then you find the common genes that are up-regulated in all the cases of interest $\endgroup$ – llrs Jan 4 '18 at 17:38
  • $\begingroup$ Oh! I didn't know that differentially downregulated genes can be found too! Thanks for your answer :D $\endgroup$ – Cookie-san Jan 4 '18 at 17:44
  • $\begingroup$ This was a comment!! You seem to need more guidance, ask your advisor or a senior people how to find the most expressed genes and from there how to find it those that are so in several stages. $\endgroup$ – llrs Jan 4 '18 at 18:17

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