Jump to ContentJump to Main Navigation

Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Stumpf, Michael P.H.

6 Issues per year

IMPACT FACTOR increased in 2014: 1.127
5-year IMPACT FACTOR: 1.537
Rank 47 out of 122 in category Statistics & Probability in the 2014 Thomson Reuters Journal Citation Report/Science Edition

SCImago Journal Rank (SJR) 2014: 0.740
Source Normalized Impact per Paper (SNIP) 2014: 0.470
Impact per Publication (IPP) 2014: 0.926

Mathematical Citation Quotient (MCQ) 2014: 0.17


Self-Organizing Maps with Statistical Phase Synchronization (SOMPS) for Analyzing Cell Cycle-Specific Gene Expression Data

Chang Sik Kim1

1Institute of Animal Resources Research, Kangwon National University

Citation Information: Statistical Applications in Genetics and Molecular Biology. Volume 7, Issue 1, ISSN (Online) 1544-6115, DOI: 10.2202/1544-6115.1323, January 2008

Publication History

Published Online:

Based on previous studies related to the yeast cell cycle, it is well known that the underlying cellular network in yeast consists of many interactions between genes that have periodic expression patterns during the cell division cycle. In this study, it is proposed that cell cycle-specific gene expression can be understood as a phenomenon of collective synchronization or, in other words, an ensemble of non-identical oscillating response signals from different systems. Therefore, we aimed to apply the theory of statistical multivariate phase synchronization to understand the cell's cyclic transcriptome as a phenomenon of collective synchronization. To this end, a novel algorithm called Self-Organizing Maps with statistical Phase Synchronization (SOMPS) is proposed and evaluated using yeast cell cycle-specific gene expression data. From the evaluation experiments, we draw the following conclusions: 1) It is possible to find groups of genes that have biological interactions with each other and significantly share gene ontology slim terms of biological processes using the theory of multivariate phase synchronization with cell cycle-specific gene expression signals; 2) Among all output clusters of SOMPS, a relatively large cluster with high periodicity with respect to its trained mean field can be considered a prominent cluster; 3) For each gene, it is possible to identify the degree of the strength of its biological interactions with other genes using the coupling strength of synchronization with its trained mean field; and 4) It is feasible to understand cell cycle-specific expression patterns as a phenomenon of collective synchronization.

Keywords: phase synchronization; cell cycle; gene expression; self-organizing map

Comments (0)

Please log in or register to comment.