All code is in R and depends on packages from CRAN and/ or Bioconductor.
Scripts to try
Genomic phylostratigraphy is a statistical approach for reconstruction of macroevolutionary trends based on the principle of founder gene formation and punctuated emergence of protein families (Domazet-Loso et al 2007). Based on this methodology it's possible to determine the age for a given gene! The scripts presented here are from an integrative analysis that uses: (1) a human tissue RNASeq dat; (2) a database of orthologous proteins that allows finding the oldest relatives to each human protein along different species; (3) the taxonomy mapping of genes to lineage clades from the NCBI Taxonomy database (www.ncbi.nlm.nih.gov/taxonomy) and; (4) the time-scale mapping provided by TimeTree resource (www.timetree.org).
Published paper: "Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes".
Script to create the plot along time-scale. You can see the plot here!
Script by clade. The plot is here!
To create the tables with the cumulative values is necessary to map the genes in the orthologous groups. The time that I was working with this I've created some mySQL databases then, it was very simple to search for the LCA. A python script to retrieve data from OMA database and other shell scripts are in this repository as an example.
Created by:
- Katia de Paiva Lopes
- Bioinformatician, PhD