Is there a way to map gene expression data from real-time PCR on gene trees?
I am trying to understand how the expression of paralogues changed over time. I have real-time PCR data and gene tree. I want to reconstruct the estimated gene expression level at each node. I don't want this to be based on only a presence/absence score, like in morphological/categorical data, but want to have expression levels that are display continuous data. This kind of work has been done for transcriptomic surveys. Do you know whether/how it can be done for realtime PCR data?
Rakesh Sharma
Select a Gene Clade from Tree:Focus on a specific functional group of genes, such as those involved in metabolism or reproduction. Collect Gene Sequences:Obtain sequences from databases like NCBI, Ensembl, or others. Construct the Gene Tree:Align sequences using tools like MUSCLE or MAFFT. Build a phylogenetic tree using RAxML, MEGA, or a similar tool. Normalize Real-Time PCR Data:Normalize expression data to account for variations, using methods like delta-delta Ct. Map Expression Data onto the Tree:Use R packages like phytools to map continuous expression data and perform ancestral state reconstruction.
Steps to Map Real-Time PCR Gene Expression Data onto a Gene Tree
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