title: Investigating the Combinatory Effects of Biological Networks on Gene Co-expression.
abstract: 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.
authors.affiliation: State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology Shanghai, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Science for Life Laboratory, KTH-Royal Institute of Technology Stockholm, Sweden.
authors.forename: Sunjae
authors.initials: S
authors.lastname: Lee
authors.affiliation: Science for Life Laboratory, KTH-Royal Institute of TechnologyStockholm, Sweden; Department of Biology and Biological Engineering, Chalmers University of TechnologyGöteborg, Sweden.
authors.forename: Adil
authors.initials: A
authors.lastname: Mardinoglu
authors.affiliation: State Key Laboratory of Bioreactor Engineering, East China University of Science and TechnologyShanghai, China; Shanghai Collaborative Innovation Center for Biomanufacturing TechnologyShanghai, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Hua
keywords: Saccharomyces cerevisiae; co-expression; co-regulation; protein-protein interaction network; transcriptional regulatory network