Investigating the Combinatory Effects of Biological Networks on Gene Co-expression

Front Physiol. 2016 May 2:7:160. doi: 10.3389/fphys.2016.00160. eCollection 2016.


Co-expressed genes often share similar functions, and gene co-expression networks have been widely used in studying the functionality of gene modules. Previous analysis indicated that genes are more likely to be co-expressed if they are either regulated by the same transcription factors, forming protein complexes or sharing similar topological properties in protein-protein interaction networks. Here, we reconstructed transcriptional regulatory and protein-protein networks for Saccharomyces cerevisiae using well-established databases, and we evaluated their co-expression activities using publically available gene expression data. Based on our network-dependent analysis, we found that genes that were co-regulated in the transcription regulatory networks and shared similar neighbors in the protein-protein networks were more likely to be co-expressed. Moreover, their biological functions were closely related.

Keywords: Saccharomyces cerevisiae; co-expression; co-regulation; protein-protein interaction network; transcriptional regulatory network.