{"id":3169,"date":"2016-10-27T11:18:57","date_gmt":"2016-10-27T10:18:57","guid":{"rendered":"http:\/\/www.blopig.com\/blog\/?p=3169"},"modified":"2016-10-27T11:19:41","modified_gmt":"2016-10-27T10:19:41","slug":"a-global-genetic-interaction-network-maps-a-wiring-diagram-of-cellular-function","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2016\/10\/a-global-genetic-interaction-network-maps-a-wiring-diagram-of-cellular-function\/","title":{"rendered":"A global genetic interaction network maps a wiring diagram of cellular function"},"content":{"rendered":"

In our last group meeting, I talked about a recent paper which presents a vast amount of genetic interaction data as well as some spatial analysis of the created data. Constanzo et al.\u00a0<\/em>used temperature-sensitive\u00a0mutant alleles to measure the interaction of ~6000 genes in the yeast Saccharomyces cerevisiae\u00a0<\/em>[1]. A typical way to analyse such data would be the use of community detection to find groups of genes with similar interaction pattern, see for example [2] for a review. Instead, the authors of this paper created a two-dimensional embedding of the network with a spring-layout, which places nodes close to each other if they show similar interaction pattern.<\/p>\n

The network layout is then compared with Gene Ontology by applying a\u00a0spatial analysis of functional enrichment (SAFE) [3]. \u00a0Clusters enriched are associated for example with cell polarity, protein degradation, and ribosomal RNA. By filtering the network for different similarities they find a hierarchical organisation of genetic function with small dense modules of pathways or complexes at the bottom and sparse clusters representing different cell compartments at the top.<\/p>\n

In this extensive paper, they then go further\u00a0into detail to quantify gene\u00a0pleiotropy, predict gene function, and how the interaction structure differs between essential and non-essential genes. They also provide that data online under\u00a0http:\/\/thecellmap.org\/costanzo2016\/ .<\/p>\n

\"(Left)<\/a>

(Left) A network of genetic interaction was embedded into a two-dimensional space using a spring-layout (Right) This embedding was compared with Gene Ontology terms to find regions of spatial enrichment.
Image from [1]<\/p><\/div>References:<\/p>\n

[1]\u00a0Costanzo, Michael, et al. “A global genetic interaction network maps a wiring diagram of cellular function.” Science 353.6306 (2016): aaf1420.<\/p>\n

[2]\u00a0Fortunato, Santo. “Community detection in graphs.” Physics Reports<\/i> 486.3 (2010): 75-174.<\/p>\n

[3]\u00a0Baryshnikova, Anastasia. “Systematic Functional Annotation and Visualization of Biological Networks.” Cell Systems<\/i> (2016).<\/p>\n","protected":false},"excerpt":{"rendered":"

In our last group meeting, I talked about a recent paper which presents a vast amount of genetic interaction data as well as some spatial analysis of the created data. Constanzo et al.\u00a0used temperature-sensitive\u00a0mutant alleles to measure the interaction of ~6000 genes in the yeast Saccharomyces cerevisiae\u00a0[1]. A typical way to analyse such data would […]<\/p>\n","protected":false},"author":34,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[10],"tags":[],"ppma_author":[522],"class_list":["post-3169","post","type-post","status-publish","format-standard","hentry","category-groupmeetings"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":522,"user_id":34,"is_guest":0,"slug":"florian-klimm","display_name":"Florian Klimm","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/c2e8e4c8d07250c3ec24ccfbc4670526fc7e55bbbb1ee1b52cae024f5c858171?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/3169","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/34"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=3169"}],"version-history":[{"count":7,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/3169\/revisions"}],"predecessor-version":[{"id":3177,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/3169\/revisions\/3177"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=3169"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=3169"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=3169"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=3169"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}