Hierarchical Community Detection on Co-expression Networks for Functional Classification of Cell-Cycle Regulated Genes of Saccharomyces cerevisiae

DOI

10.2991/978-94-6463-684-0_14How to use a DOI?

Keywords

Networks; Community Detection; Gene Co-expression; Hierarchical Structures; Saccharomyces cerevisiae; Biological Networks; Modularity; Closeness Centrality; Adjusted Rand Index (ARI)

Abstract

This study explored hierarchical community detection in gene co-expression networks to enhance the functional classification of cellcycle regulated genes in Saccharomyces cerevisiae. We evaluated three hierarchical community detection algorithms—Girvan-Newman (GN), Paris, and Local Optimization Function Model (LFM)—on a gene coexpression network of Saccharomyces cerevisiae. Our findings showed that the GN algorithm effectively identified distinct community structures at various hierarchical levels, demonstrating high modularity and closeness centrality. The Paris algorithm provided a comprehensive view of the network’s hierarchical structure, while the LFM algorithm revealed detailed sub-communities sensitive to the alpha parameter. The study’s results were validated using modularity, closeness centrality, and the Adjusted Rand Index (ARI), highlighting their potential applications in genomics and cellular biology. This research advanced the field by presenting new perspectives and methods for biological network analysis, paving the way for more targeted and effective approaches to understanding gene functions.

Copyright

© 2025 The Author(s)

Open Access

Open Access This chapter is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/), which permits any noncommercial use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made.

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TY  - CONF
AU  - Jaimielle Kyle Calderon
AU  - Princess Angel Ventures
AU  - Jhoirene Clemente
PY  - 2025
DA  - 2025/04/30
TI  - Hierarchical Community Detection on Co-expression Networks for Functional Classification of Cell-Cycle Regulated Genes of Saccharomyces cerevisiae
BT  - Proceedings of the  Workshop on Computation: Theory and Practice (WCTP 2024)
PB  - Atlantis Press
SP  - 215
EP  - 234
SN  - 2589-4900
UR  - https://doi.org/10.2991/978-94-6463-684-0_14
DO  - 10.2991/978-94-6463-684-0_14
ID  - Calderon2025
ER  -