Exploiting bounded signal flow for graph orientation based on cause–effect pairs.docVIP

下载本文档

3
0
约5.7万字
约 12页
2017-05-16 发布于上海
举报
版权申诉

Exploiting bounded signal flow for graph orientation based on cause–effect pairs.doc

1、本文档共12页，可阅读全部内容。
2、原创力文档（book118）网站文档一经付费（服务费），不意味着购买了该文档的版权，仅供个人/单位学习、研究之用，不得用于商业用途，未经授权，严禁复制、发行、汇编、翻译或者网络传播等，侵权必究。
3、本站所有内容均由合作方或网友上传，本站不对文档的完整性、权威性及其观点立场正确性做任何保证或承诺！文档内容仅供研究参考，付费前请自行鉴别。如您付费，意味着您自己接受本站规则且自行承担风险，本站不退款、不进行额外附加服务；查看《如何避免下载的几个坑》。如果您已付费下载过本站文档，您可以点击这里二次下载。
4、如文档侵犯商业秘密、侵犯著作权、侵犯人身权等，请点击“版权申诉”（推荐），也可以打举报电话：400-050-0827(电话支持时间：9:00-18:30)。
5、该文档为VIP文档，如果想要下载，成为VIP会员后，下载免费。
6、成为VIP后，下载本文档将扣除1次下载权益。下载后，不支持退款、换文档。如有疑问请联系我们。
7、成为VIP后，您将拥有八大权益，权益包括：VIP文档下载权益、阅读免打扰、文档格式转换、高级专利检索、专属身份标志、高级客服、多端互通、版权登记。
8、VIP文档为合作方或网友上传，每下载1次，网站将根据用户上传文档的质量评分、类型等，对文档贡献者给予高额补贴、流量扶持。如果你也想贡献VIP文档。上传文档

Exploiting bounded signal flow for graph orientation based on cause–effect pairs

Dornetal.AlgorithmsforMolecularBiology2011,6:21 /content/6/1/21 RESEARCH OpenAccess Exploitingboundedsignalflowforgraph orientationbasedoncause–effectpairs BrittaDorn1,FalkHüffner2*,DominikusKrüger3,RolfNiedermeier2andJohannesUhlmann2 Abstract Background:Weconsiderthefollowingproblem:Givenanundirectednetworkandasetofsender–receiverpairs, directalledgessuchthatthemaximumnumberof“signalflows”definedbythepairscanberoutedrespecting edgedirections.Thisproblemhasapplicationsinunderstandingproteininteractionbasedcellregulation mechanisms.SincethisproblemisNP-hard,researchsofarconcentratedonpolynomial-timeapproximation algorithmsandtractablespecialcases. Results:Wetaketheviewpointofparameterizedalgorithmicsandexamineseveralparametersrelatedtothe maximumsignalflowoververticesoredges.Weprovideseveralfixed-parametertractabilityresults,andinone caseasharpcomplexitydichotomybetweenalinear-timesolvablecaseandaslightlymoregeneralNP-hardcase. Weexaminethevalueoftheseparametersforseveralreal-worldnetworkinstances. Conclusions:SeveralbiologicallyrelevantspecialcasesoftheNP-hardproblemcanbesolvedtooptimality.Inthis way,parameterizedanalysisyieldsbothdeeperinsightintothecomputationalcomplexityandpracticalsolving strategies. Background ×V be a set of ordered source–target pairs, which we Current technologies [1] like two-hybrid screening can sometimes refer to as “signals”. In order to distinguish find protein interactions, leading to protein-protein pairsfromedgesorarcs,weusethenotation[a,b]?P interaction(PPI)networks,butcannotdecidethedirec- todenotethepairstartinginaandendinginb.Wesay tion of the interaction. This can be complemented by that a pair [a,b] ?Pis satisfied by agiven orientation geneknock-out experiments which constitute a way to G if there exists a directed path from a to b in . The G determinecausal relations inthesenetworks, thuspro- central problem considered in this work is to find an viding additional information on possible directions of orientatio