Plastid-nuclear ERCnet analysis results

Plant cells rely on an interconnected network of proteins interacting at many levels (e.g. physical enzyme complexes, gene regulatory modules, and biosynthetic pathways). Pairs of proteins that interact at any of these levels have been shown to exhibit phylogenetic signatures of evolutionary rate covariation (ERC), providing a basis for detecting functional interactions among proteins. Here, we apply ERCnet, a bioinformatic tool for performing genome-scale ERC analyses, to predict a plant protein-protein interactome network. We find a clustered set of proteins that exhibit strong signatures of ERC with the plastid caseinolytic protease (Clp) and other plastid proteostasis components, thus forming a functional module within the network. In addition to including proteins with known or predicted functions in protein import, transcription, translation, and degradation in plastids, the module also includes proteins with previously unknown molecular function, thus providing evidence that thes..., The data included here are the output of the ERCnet program. See the ERCnet GItHub page (https://github.com/EvanForsythe/ERCnet) for deteailed descriptions of outfile files., , # Plastid-nuclear ERCnet analysis results

[https://doi.org/10.5061/dryad.hx3ffbgp7](https://doi.org/10.5061/dryad.hx3ffbgp7)

## Description of the data and file structure

The data deposited here are a zipped folder containing several subfolders. These folders contain the output files and metadata from the ERCnet program.

### Files and variables

#### File: OUT_ERC_Final.zip

**Description:** 

From ERCnet GitHub README (release v1.1.0):

Below is a brief description of each of the files and subdirectories that are output during a run of ERCnet. Many of the files created are intermediate files, which you likely will not need to inspect. Directories are shown in the order in which they're created during the ERCnet workflow.

* `ERCnet-1.1.0.zip`: contains a clone of the ERCnet code used for this analysis.
* `Species_mapping.csv`: shows how ERCnet recognizes species IDs
* `Seq_counts_per_species.csv`: shows how many homologs from each species were found in each gene family
* `SpeciesT...,