xudeh / d.radiodurans_ppi_rwr_hd

This repository contains the R code and Cytoscape files that were used for the project in the MSB course Network Biology.

D.radiodurans_PPI_RWR_HD

This repository contains the R code and Cytoscape files that were used for the project in the MSB course Network Biology.

Project code.R contains the R script that was used to extract the giant component from the filtered networks.

The following 3 files contain the full subnetworks for each of the proteins (integer in title correspons to confidence cut-off; e.g. 900 = 0.9 and above)

Analysis of RecA - 950_Deinococcus_radiodurans.sif Analysis of UvrC - 900_Deinococcus_radiodurans.sif Analysis of PprA - 700_Deinococcus_radiodurans.sif

The following 3 files contain the giant component for each of the subnetworks. The Random walk with restart and Heat diffusion algorithms were performed using these subnetworks:

Analysis of RecA - N950_giant.sif Analysis of UvrC - N900_giant.sif Analysis of PprA - N700_giant.sif

Top 20 protein networks:

PprA_RWR_20proteins.sif RecA_RWR_20proteins.sif UvrC_RWR_20proteins.sif

Supplementary materials 1.rar - contains the tables with final sorted probabilities for the three proteins as source nodes Supplementary materials 2.rar - contains the full GO enrichment analysis list for the RecA and UvrC RWR results Supplementary materials 3.txt - contains the additional GO enrichment analysis performed on the lower cluster of the RecA visualization.

All plots can be generated by running the Project code.R file