{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T10:19:25Z","timestamp":1769941165052,"version":"3.49.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Microarray-based gene expression data have been generated widely to study different biological processes and systems. Gene co-expression networks are often used to extract information about groups of genes that are \u2018functionally\u2019 related or co-regulated. However, the structural properties of such co-expression networks have not been rigorously studied and fully compared with known biological networks. In this article, we aim at investigating the structural properties of co-expression networks inferred for the species Saccharomyces Cerevisiae and comparing them with the topological properties of the known, well-established transcriptional network, MIPS physical network and protein\u2013protein interaction (PPI) network of yeast.<\/jats:p>\n               <jats:p>Results: These topological comparisons indicate that co-expression networks are not distinctly related with either the PPI or the MIPS physical interaction networks, showing important structural differences between them. When focusing on a more literal comparison, vertex by vertex and edge by edge, the conclusion is the same: the fact that two genes exhibit a high gene expression correlation degree does not seem to obviously correlate with the existence of a physical binding between the proteins produced by these genes or the existence of a MIPS physical interaction between the genes. The comparison of the yeast regulatory network with inferred yeast co-expression networks would suggest, however, that they could somehow be related.<\/jats:p>\n               <jats:p>Conclusions: We conclude that the gene expression-based co-expression networks reflect more on the gene regulatory networks but less on the PPI or MIPS physical interaction networks.<\/jats:p>\n               <jats:p>Contact: \u00a0hongzhe@mail.med.upenn.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp632","type":"journal-article","created":{"date-parts":[[2009,11,13]],"date-time":"2009-11-13T01:15:00Z","timestamp":1258074900000},"page":"205-214","source":"Crossref","is-referenced-by-count":54,"title":["Co-expression networks: graph properties and topological comparisons"],"prefix":"10.1093","volume":"26","author":[{"given":"Ramon","family":"Xulvi-Brunet","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]},{"given":"Hongzhe","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,11,12]]},"reference":[{"key":"2023012508215007300_B1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1103\/RevModPhys.74.47","article-title":"Statistical mechanics of complex networks","volume":"74","author":"Albert","year":"2002","journal-title":"Rev. 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