Evolutionary rate covariation reveals novel protein networks in Mycobacterium tuberculosis

Proteins that participate together in a function often show covariation in their relative evolutionary rates, because selective pressures influencing their evolution affect co-functional proteins as an ensemble. Evolutionary Rate Covariation (ERC) is a computational comparative genomics tool that identifies this co-variation using collections of orthologous gene sequences from several species, providing measures of correlation that can be used to infer novel functional relationships. Though proven to be successful at identifying novel functional relationships in eukaryotic species, ERC’s usefulness in prokaryotes requires further investigation. In this study, we validate the use of ERC in prokaryotes using 106 species in the Mycobacterium genus, and provide a useful genome-wide dataset of functional relationships between 11,638 mycobacterial orthologous gene groups with Mycobacterium tuberculosis as a focal model organism. To evaluate the dataset’s utility, we studied genome-wide ERC pa..., , # Mycobacterium Tuberculosis ERC data

[Access this dataset on Dryad](https://doi.org/10.5061/dryad.v41ns1s8v)

This README file descibes all of the data gathered and code used in this ERC study. All of the ERC data for the gene families, networks, and operons discussed in the manuscript, as well as all other underlying data and materials used, are stored here.

## Data Access

### Myco_Proteomes

* Full FASTA RefSeq amino acid sequences for each mycobacterium species used in this study
* Obtained from the National Center for Biotechnology Information
* .csv and .pdf versions of a table containing each species name, accession number, genome version, and number of protein coding genes

### Orthogroup_Seqeunces

* Amino acids sequences for each orthogroup created from OrthoFinder

### Gene_Trees

* Gene trees corresponding to each orthogroup generated by Orthofinder

### SpeciesTree_Rooted.tree

* Master species tree of all mycobacterium species used in this study generated by OrthoFinder...,