Abstract </head> <body text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#CF30CF" alink="#FF0000" nosave> <br> <center><h2> Signed Weighted Gene Coexpression Network Analysis </h2> <br> <h2> Michael Mason </h2> <h3> (UC Los Angeles) </h3> </center> <br> <b>Background:</b> Network methods are increasingly utilized to explore the relationships and interaction of genes and/or proteins. Genes or proteins that share a common neighborhood may also share a common biological function or pathway. Recently, weighted gene coexpression network analysis (WGCNA) has successfully yielded system’s level understandings from global gene expression data. This method uses unsigned correlations to describe gene or protein interactions and cluster them together. Leveraging signed interactions may yield more biologically interesting results. Here we incorporate signed gene interactions with WGCNA to investigate the biological relevance of signed networks in glioblastoma and mouse embryonic stem cells. <p> <b>Results:</b> To extend WGCNA methods to include signed correlations, we map the signed correlations which range from [-1, 1] to a range of [0, 1]. This mapping preserves the continuous nature of the weighting allowing WGCNA methods such as the topological overlap matrix by Ravasz et al. to be used. Using this adjacency matrix, we show network concepts such as the cluster coefficient and scale free topology criterion remain intact. We also show that signed WGCNA preserves large modules found via unsigned WCGNA while finding new modules. Furthermore, we incorporate ChIP-Pet data from mouse embryonic stem cells showing that for some datasets signed WGCNA out performs unsigned WCGNA by clustering genes or proteins into more biologically interesting modules. <p><b>Conclusion:</b>Signed weighted gene coexpression network analysis can facilitate a system’s level understanding of gene and/or protein interactions. <br><br><br> <a href="index.html">Back to main page</a><br><br> <hr> <p><br><br>  <script type="text/javascript"> var sc_project=2800657; var sc_invisible=0; var sc_partition=28; var sc_security="dd1187b0"; </script> <script type="text/javascript" src="http://www.statcounter.com/counter/counter_xhtml.js"></script><noscript><div class="statcounter"><a class="statcounter" href="http://www.statcounter.com/"><img class="statcounter" src="http://c29.statcounter.com/2800657/0/dd1187b0/0/" alt="free stats" /></a></div></noscript>  </body> </html>