{"id":319,"date":"2018-06-08T10:06:13","date_gmt":"2018-06-08T17:06:13","guid":{"rendered":"http:\/\/blogs.reed.edu\/compbio\/?p=319"},"modified":"2018-06-08T10:06:13","modified_gmt":"2018-06-08T17:06:13","slug":"week-2-sinksource-and-aucs","status":"publish","type":"post","link":"https:\/\/blogs.reed.edu\/compbio\/2018\/06\/08\/week-2-sinksource-and-aucs\/","title":{"rendered":"Week 2:  Sinksource+ and AUCs"},"content":{"rendered":"<p>We found an algorithm that solves the edge case problem. Sinksource+ removes the negatives and adds one negative to every single node. The weight of the edge is also a constant, which means that it&#8217;s the same for a node of any degree. This significantly devalues nodes that aren&#8217;t very well connected and would not be suitable for polygenic analysis.<\/p>\n<p>However, it works horrendously in a single layer method with no prime nodes. The AUC sticks at around 0.5, which is the worst possible AUC you can have. However, it works great in a two layer network, giving our SZ network a score of 0.65. If you add negatives back in with the addition of sinksource+ and reduce the sinksource+ constant, we get an SZ AUC of 0.675 and a cell motility AUC of 0.801, which is the best AUC we have seen for an SZ gene identifier. I&#8217;m also running the program on the autism positives right now, and it appears that the AUC is running at about similar levels to where they were with E1 and E2.<\/p>\n<p><img decoding=\"async\" class=\"max-width\" src=\"https:\/\/media.springernature.com\/m685\/nature-assets\/neuro\/journal\/v19\/n11\/images\/nn.4353-F2.jpg\" alt=\"Figure 2\" \/><\/p>\n<div class=\"csl-bib-body\">\n<div class=\"csl-entry\">\n<div class=\"csl-right-inline\">Krishnan, A. <i>et al.<\/i>Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. <i>Nature Neuroscience<\/i><b>19,<\/b>1454 (2016).<\/div>\n<\/div>\n<\/div>\n<div><\/div>\n<div>I think we are at the point where we will begin writing the paper. These results are a satisfying in that it&#8217;s probably just the nature of SZ that genes implicated are going to be difficult and somewhat disparately related. That&#8217;s not necessarily a bad thing. Polygenic positives are by definition only contributing slightly towards a disease. The strongest p-value for a SNP in an SZ GWAS has a frequency of 0.765 in SZ participants and a frequency of 0.75 in control participants. A low AUC in an SZ gene labeler is almost expected.<\/div>\n<div><\/div>\n<div>Goals for next week: Write the paper<\/div>\n<div><\/div>\n","protected":false},"excerpt":{"rendered":"<p>We found an algorithm that solves the edge case problem. Sinksource+ removes the negatives and adds one negative to every single node. The weight of the edge is also a constant, which means that it&#8217;s the same for a node of any degree. This significantly devalues nodes that aren&#8217;t very well connected and would not &hellip; <a href=\"https:\/\/blogs.reed.edu\/compbio\/2018\/06\/08\/week-2-sinksource-and-aucs\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Week 2:  Sinksource+ and AUCs&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1584,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-319","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/319","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/users\/1584"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/comments?post=319"}],"version-history":[{"count":1,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/319\/revisions"}],"predecessor-version":[{"id":320,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/posts\/319\/revisions\/320"}],"wp:attachment":[{"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/media?parent=319"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/categories?post=319"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.reed.edu\/compbio\/wp-json\/wp\/v2\/tags?post=319"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}