Investigating the Combinatory Effects of Biological Networks on Gene Co-expression
Journal article, 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 Saccharornyces 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.


transcriptional regulatory network



Saccharomyces cerevisiae


C. Zhang

East China University of Science and Technology

SangWook Lee

Royal Institute of Technology (KTH)

Adil Mardinoglu

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Q. Hua

Shanghai Collaborative Innovation Center for Biomanufacturing Technology

East China University of Science and Technology

Frontiers in Physiology

1664-042X (ISSN)

Vol. 7 MAY 160

Subject Categories

Bioinformatics and Systems Biology



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