Multispecies comparison of transcriptome expression data correcting using control group
0
1
Entering edit mode
2.1 years ago
T_18 ▴ 40

Dear all,

I’m currently working on a multispecies comparison of RNAseq transcriptome data and I would like to get your input for the design of my analysis steps.

I am comparing 4 species on 3 different hosts and 1 control. So in total I am comparing 16 groups with a control for each species. I am thinking to analyse my transcript expression data similarly as I do with other datapoints I measured: I have taken some measurements of the specimens to quantify performance, for correct comparisons of these measurements I corrected these values based on the values in the control group. Simply because each species has a different (species-specific) response, I correct using the values of the control group so you can directly compare the values of the different species. I am thinking to do the same for the gene expression data, and for this I would like to get your thoughts.

In the meantime I have read a lot of comparative papers (e.g. as covered in this discussion: https://www.biostars.org/p/358805/) and the very first step is determining what the ‘same’ genes are (e.g. by blast using a reference database or orthologue analysis). After this, many studies do a co-expression analysis of all gene expression data combined, or something similar but I do not really see the use of this for my data. These papers are e.g. comparing tissue type in different species without having a “neutral” control group.

I would like to get your views on this. To be a bit more focussed, my main issues:

  • Given my dataset, I want to correct the expression data of similar genes (based on ID/orthology) using the expression level in the control groups for each species as a correction for a direct comparison between species.

    • Perhaps you are aware of a good recent paper dealing with multispecies comparison that take a different approach than ‘identification -> co-expression’?

Thanks a lot in advance!

RNA-Seq multispecies comparison DGE • 541 views
ADD COMMENT

Login before adding your answer.

Traffic: 1901 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6