{"id":930,"date":"2007-04-25T19:10:47","date_gmt":"2007-04-25T18:10:47","guid":{"rendered":"http:\/\/www.wjst.de\/blog\/2007\/04\/25\/hubs-and-superhubs-in-asthma-low-activity\/"},"modified":"2007-04-27T10:18:47","modified_gmt":"2007-04-27T09:18:47","slug":"hubs-and-superhubs-in-asthma-low-activity","status":"publish","type":"post","link":"https:\/\/www.wjst.de\/blog\/sciencesurf\/2007\/04\/hubs-and-superhubs-in-asthma-low-activity\/","title":{"rendered":"Hubs and superhubs in asthma: low activity"},"content":{"rendered":"<p>Here comes the reference to a first <a href=\"http:\/\/www.nature.com\/msb\/journal\/v3\/n1\/full\/msb4100138.html\">molecular system biology paper<\/a> on asthma &#8211; something on my to-do list for 3 years. The authors constructed a biological interaction network using a database of curated molecular interactions.<!--more-->In a next step they mapped differentially expressed genes from microarray data and analyzed the correlation between the topology and biological function using gene ontologies.<br \/>\nHubs are defined as nodes with a connectivity greater than 5 (they found 88 hubs, mostly evolutionary late genes, seven were significantly modulated but I couldn\u00c2\u00b4t find out which genes). Superhubs are those with a connectivity of >5 in the shortest path connecting hubs (16 found, mainly evolutionary ancient processes, all with a small dynamic range).<br \/>\nSo far, the model comprises only BALB\/c and RAG KO mice &#8211; I am sure that this exercise will soon be repeated for human lungs.<br \/>\nI wonder why they haven&#8217;t identified more transcription factors &#8211; is the rather unorthodox definition of hubs responsible for that? An alternative option could take into account the hierarchical (or temporal?) relationship of nodes. Even then might be only a small overlap between affected genes and binding targets as noticed in a recent <a href=\"http:\/\/www.nature.com\/ng\/journal\/v39\/n5\/abs\/ng2012.html\">yeast<\/a> paper.<\/p>\n<blockquote><p>\nFirst, a transcription factor can regulate secondary targets via regulatory cascades. Therefore, the unrefined knockout targets are likely to include both direct and indirect targets. Second, different transcription factors occupying a promoter could compensate for each other&#8217;s loss, masking the deletion effect. Finally, a transcription factor could bind a promoter under normal growth conditions but function only under specific environmental conditions&#8230;\n<\/p><\/blockquote>\n<p>scienceblog:doi:10.1038\/msb4100138<br \/>\nscienceblog:doi:10.1038\/ng2012<\/p>\n\n<p>&nbsp;<\/p>\n<div class=\"bottom-note\">\n  <span class=\"mod1\">CC-BY-NC Science Surf , accessed 06.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"<p>Here comes the reference to a first molecular system biology paper on asthma &#8211; something on my to-do list for 3 years. The authors constructed a biological interaction network using a database of curated molecular interactions. &nbsp; CC-BY-NC Science Surf , accessed 06.04.2026<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8,2],"tags":[],"class_list":["post-930","post","type-post","status-publish","format-standard","hentry","category-asthma-allergy","category-genetics-biology"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/930","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=930"}],"version-history":[{"count":0,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/930\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=930"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=930"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=930"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}