%A Zhang,Cheng %A Lee,Sunjae %A Mardinoglu,Adil %A Hua,Qiang %D 2016 %J Frontiers in Physiology %C %F %G English %K Saccharomyces cerevisiae,co-expression,co-regulation,Transcriptional regulatory network,Protein-protein interaction network %Q %R 10.3389/fphys.2016.00160 %W %L %M %P %7 %8 2016-May-02 %9 Original Research %+ Adil Mardinoglu,Science for Life Laboratory, KTH-Royal Institute of Technology,Stockholm, Sweden,adilm@scilifelab.se %+ Adil Mardinoglu,Department of Biology and Biological Engineering, Chalmers University of Technology,Göteborg, Sweden,adilm@scilifelab.se %+ Qiang Hua,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology,Shanghai, China,qhua@ecust.edu.cn %+ Qiang Hua,Shanghai Collaborative Innovation Center for Biomanufacturing Technology,Shanghai, China,qhua@ecust.edu.cn %# %! Combinatory effects of biological networks %* %< %T Investigating the Combinatory Effects of Biological Networks on Gene Co-expression %U https://www.frontiersin.org/articles/10.3389/fphys.2016.00160 %V 7 %0 JOURNAL ARTICLE %@ 1664-042X %X 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.