cluster2hub: for the identification of hubs in the gene co-expression cluster network

This pipeline identifies transcription factors, kinases and other proteins as hubs in the networks of gene co-expression clusters. I present an integrative approach to construct protein interactions networks of transcription factors, kinases and proteins of optimal gene co-expression clusters and identify functional annotations and pathways and drug chemical interactions of hubs.

Requirements

• Python: clust
• R: igraph, enrichR
• PERL
• Live connection

Installation

sudo chmod +x -R cluster2hub/Scripts/*
echo 'export PATH="your-dir/cluster2hub/Scripts/:$PATH"' >> ~/.bashrc
source ~/.bashrc

Usage

Usage: cluster2hub [-h] [-f <file>] [-r <replicates>] [-p <ppis>] [-t <hubs>] [-i <interactions>] [-d <directory>]
positional arguments:
	-f <file>			: Input expression file
	-p <ppis>			: Protein-proteins interactions file
optional arguments:
	-h, --help			: Shows this help message and exit
	-r <replicates>			: Replicates structure file
	-t <hubs>			: Percent of top degree nodes, default = 5
	-i <interactions>		: Drug gene interactions file
	-d <directory>			: Output directory
Others: Tfs.R <directory>
	Tfs_all.pl <directory>
	Kinases.R <directory>
	Kinases_all.pl <directory>
	Tfs_all_ppis.pl <directory> <ppis>
	Kinases_all_ppis.pl <directory> <ppis>
	Networks.R <directory> <hubs>
	Go_kegg.R <directory>
	Dgi.pl <directory> <interactions>

Example

cluster2hub -f Test.txt -r Test_replicates.txt -p PPIs.txt -t 2 -i dgi.tsv -d Cluster2hub_out

The example figures:

Figure 1.png

Figure 1: Clusters plot.

Figure 2.png

Figure 2: Clusters 0 protein interactions network. Burlywood nodes are transcription factors, skyblue are kinases and darkolivegreen nodes are the proteins in the Cluster 0.

Figure 3.png

Figure 3: Clusters 1 protein interactions network. Burlywood nodes are transcription factors, skyblue are kinases and darkolivegreen nodes are the proteins in the Cluster 1.

References

• Basel Abu-Jamous and Steven Kelly (2018) Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data. Genome Biology 19:172; doi: https://doi.org/10.1186/s13059-018-1536-8.
• Wajid Jawaid (2021). enrichR: Provides an R Interface to 'Enrichr'. R package version 3.0. https://CRAN.R-project.org/package=enrichR
• Csardi G, Nepusz T: The igraph software package for complex network research, InterJournal, Complex Systems 1695. 2006. https://igraph.org