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Investigating the Combinatory Effects of Biological Networks on Gene Co-expression
KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-6428-5936
KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Chalmers, Dept Biol & Biol Engn, Sweden.
2016 (English)In: Frontiers in Physiology, ISSN 1664-042X, E-ISSN 1664-042X, Vol. 7, 160Article in journal (Refereed) PublishedText
Abstract [en]

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.

Place, publisher, year, edition, pages
Frontiers Media , 2016. Vol. 7, 160
Keyword [en]
Saccharomyces cerevisiae, co-expression, co-regulation, transcriptional regulatory network, protein-protein interaction network
National Category
Bioinformatics and Systems Biology Physiology
Identifiers
URN: urn:nbn:se:kth:diva-187330DOI: 10.3389/fphys.2016.00160ISI: 000375185600001OAI: oai:DiVA.org:kth-187330DiVA: diva2:930110
Funder
Knut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20160523

Available from: 2016-05-23 Created: 2016-05-20 Last updated: 2016-05-23Bibliographically approved

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