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# Support code for Ncube-Kanyika et.al. (2022) CASSAVA PROTEINS INTERACTING WITH THE MOVEMENT PROTEIN OF SOUTH AFRICAN CASSAVA MOSAIC VIRUS REVEAL ROLES IN PATHOGENICITY.

By Valeria Velásquez-Zapata

Overview

This repository contains code for performing the bioinformatic analysis of the manuscript. It is separated in two R scripts with instruction on how to format the files to run the SAINTexpress and Y2H-SCORES software in analysis of MS Co-IP data and for posterior network analysis .

Citations

If you use part of this code please cite

  • Ncube-Kanyika B, Velásquez-Zapata V, Wise RP, Rey MEC (2022). Cassava proteins interacting with the movement protein of south African cassava mosaic virus reveal roles in pathogenicity.

Software requirements

  • R
  • R packages: UniprotR, stringr, reshape2, tidyverse, psych, DESeq2, mass, igraph, RCy3
  • Unix

Functions in this repository

Two R files were created with the main functions used to perform the analysis. A brief description of each file is provided:

  1. SAINTexpress and Y2H-SCORES analyses.R contains the formatting of files to run SAINTexpress and Y2H-SCORES.

  2. BC1_subnetwork_analysis.R contains network analysis of the BC1 interactors in a compiled Arabidopsis interactome.

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