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 language | English |
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Title of host publication | Computing in Cardiology 2016 |
Subtitle of host publication | Volume 43 |
Place of Publication | United States |
Publisher | IEEE, Institute of Electrical and Electronics Engineers |
Pages | 353-355 |
Number of pages | 3 |
Volume | 43 |
ISBN (Electronic) | 9781509008957 |
ISBN (Print) | 9781509008964 |
Publication status | Published - 2016 |
Event | 43rd Computing in Cardiology Conference, CinC 2016 - Marriot Hotel and Simon Fraser University, Vancouver, Canada Duration: 11 Sep 2016 → 14 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
Conference | 43rd Computing in Cardiology Conference, CinC 2016 |
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Country/Territory | Canada |
City | Vancouver |
Period | 11/09/16 → 14/09/16 |
Other | Computing 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. |
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