GraphBreak: Tool for Network Community based Regulatory Medicine, Gene co-expression, Linkage Disequilibrium analysis, functional annotation and more

TL;DR

GraphBreak is a versatile tool for community detection in biological networks, aiding functional annotation and disease association analysis, with potential applications in gene regulation, co-expression, and protein interactions.

Contribution

It introduces a novel integrated algorithmic suite for community detection and functional analysis in various biological networks, improving disease gene prioritization.

Findings

Effective in detecting communities with disease over-representation

Facilitates prioritization of target genes for drug repositioning

Applicable to diverse network types beyond eQTL data

Abstract

Graph network science is becoming increasingly popular, notably in big-data perspective where understanding individual entities for individual functional roles is complex and time consuming. It is likely when a set of genes are regulated by a set of genetic variants, the genes set is recruited for a common or related functional purpose. Grouping and extracting communities from network of associations becomes critical to understand system complexity, thus prioritizing genes for dis-ease and functional associations. Workload is reduced when studying entities one at a time. For this, we present GraphBreak, a suite of tools for community detection application, such as for gene co-expression, protein interaction, regulation network, etc.Although developed for use case of eQTLs regulatory genomic net-work community study -- results shown with our analysis with sample eQTL data. Graphbreak can be deployed for other studies if input data has been fed in requisite format, including but not limited to gene co-expression networks, protein-protein interaction network, signaling pathway and metabolic network. Graph-Break showed critical use case value in its downstream analysis for disease association of communities detected. If all independent steps of community detection and analysis are a step-by-step sub-part of the algorithm, GraphBreak can be considered a new algorithm for community based functional characterization. Combination of various algorithmic implementation modules into a single script for this purpose illustrates GraphBreak novelty. Compared to other similar tools, with GraphBreak we can better detect communities with over-representation of its member genes for statistical association with diseases, therefore target genes which can be prioritized for drug-positioning or drug-re-positioning as the case be.