Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis

13Citations
Citations of this article
44Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

Discovering disease-associated genes (DG) is strategic for understanding pathological mechanisms. DGs form modules in protein interaction networks and diseases with common phenotypes share more DGs or have more closely interacting DGs. This prompted the development of Specific Betweenness (S2B) to find genes associated with two related diseases. S2B prioritizes genes frequently and specifically present in shortest paths linking two disease modules. Top S2B scores identified genes in the overlap of artificial network modules more than 80% of the times, even with incomplete or noisy knowledge. Applied to Amyotrophic Lateral Sclerosis and Spinal Muscular Atrophy, S2B candidates were enriched in biological processes previously associated with motor neuron degeneration. Some S2B candidates closely interacted in network cliques, suggesting common molecular mechanisms for the two diseases. S2B is a valuable tool for DG prediction, bringing new insights into pathological mechanisms. More generally, S2B can be applied to infer the overlap between other types of network modules, such as functional modules or context-specific subnetworks. An R package implementing S2B is publicly available at https://github.com/frpinto/S2B.

References Powered by Scopus

The human disease network

2698Citations
N/AReaders
Get full text

Towards a proteome-scale map of the human protein-protein interaction network

2418Citations
N/AReaders
Get full text

A proteome-scale map of the human interactome network

1037Citations
N/AReaders
Get full text

Cited by Powered by Scopus

Computational network biology: Data, models, and applications

151Citations
N/AReaders
Get full text

MODifieR: An Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks

13Citations
N/AReaders
Get full text

Systems biology: A powerful tool for drug development

12Citations
N/AReaders
Get full text

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Cite

CITATION STYLE

APA

Garcia-Vaquero, M. L., Gama-Carvalho, M., Rivas, J. D. L., & Pinto, F. R. (2018). Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-29990-7

Readers' Seniority

Tooltip

PhD / Post grad / Masters / Doc 18

67%

Researcher 7

26%

Professor / Associate Prof. 2

7%

Readers' Discipline

Tooltip

Biochemistry, Genetics and Molecular Bi... 15

63%

Neuroscience 4

17%

Computer Science 3

13%

Agricultural and Biological Sciences 2

8%

Article Metrics

Tooltip
Social Media
Shares, Likes & Comments: 1

Save time finding and organizing research with Mendeley

Sign up for free