A heuristic gene regulatory networks model for cardiac function and pathology

Armita Zarnegar, Peter Vamplew, Andrew Stranieri, Herbert F. Jelinek

Research output: Book chapter/Published conference paperConference paperpeer-review

2 Citations (Scopus)

Abstract

Genome-wide association studies (GWAS) and next-generation sequencing (NGS) has led to an increase in information about the human genome and cardiovascular disease. Understanding the role of genes in cardiac function and pathology requires modeling gene interactions and identification of regulatory genes as part of a gene regulatory network (GRN). Feature selection and data reduction not sufficient and require domain knowledge to deal with large data. We propose three novel innovations in constructing a GRN based on heuristics. A 2D Visualised Co-regulation function. Post-processing to identify gene-gene interactions. Finally a threshold algorithm is applied to identify the hub genes that provide the backbone of the GRN. The 2D Visualized Co-regulation function performed significantly better compared to the Pearson's correlation for measuring pairwise associations (t=3.46, df=5, p=0.018). The F-measure, improved from 0.11 to 0.12. The hub network provided a 60% improvement to that reported in the literature. The performance of the hub network was then also compared against ARACNe and performed significantly better (p=0.024). We conclude that a heuristics approach in developing GRNs has potential to improve our understanding of gene regulation and interaction in diverse biological function and disease.
Original languageEnglish
Title of host publicationComputing in Cardiology 2016
Subtitle of host publicationVolume 43
Place of PublicationUnited States
PublisherIEEE, Institute of Electrical and Electronics Engineers
Pages353-355
Number of pages3
Volume43
ISBN (Electronic)9781509008957
ISBN (Print)9781509008964
Publication statusPublished - 2016
Event43rd Computing in Cardiology Conference, CinC 2016 - Marriot Hotel and Simon Fraser University, Vancouver, Canada
Duration: 11 Sep 201614 Sep 2016
https://web.archive.org/web/20170603121743/http://cinc2016.org (Conference website)
http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=7861973 (Conference proceedings)

Conference

Conference43rd Computing in Cardiology Conference, CinC 2016
Country/TerritoryCanada
CityVancouver
Period11/09/1614/09/16
OtherComputing in Cardiology provides an international forum for scientists and professionals from the fields of medicine, physics, engineering and computer science, and has been held annually since 1974.
Internet address

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