Assessment of Algorithms for Inferring Positional Weight Matrix Motifs of Transcription Factor Binding Sites Using Protein Binding Microarray Data 英文参考文献.docVIP
- 1、本文档共8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
查看更多
Assessment of Algorithms for Inferring Positional Weight Matrix Motifs of Transcription Factor Binding Sites Using Protein Binding Microarray Data 英文参考文献
AssessmentofAlgorithmsforInferringPositionalWeight
MatrixMotifsofTranscriptionFactorBindingSitesUsing
ProteinBindingMicroarrayData
YaronOrenstein,ChaimLinhart,RonShamir*
BlavatnikSchoolofComputerScience,Tel-AvivUniversity,Tel-Aviv,Israel
Abstract
Thenewtechnologyofproteinbindingmicroarrays(PBMs)allowssimultaneousmeasurementofthebindingintensitiesofa
transcription factor totens of thousands of synthetic double-stranded DNA probes, covering all possible 10-mers. A key
computational challenge is inferring the binding motif from these data. We present a systematic comparison of four
methodsdevelopedspecificallyforreconstructingabindingsitemotifrepresentedasapositionalweightmatrixfromPBM
data. The reconstructed motifs were evaluated in terms of three criteria: concordance with reference motifs from the
literatureandabilitytopredictinvivoandinvitrobindings.Theevaluationencompassedover200transcriptionfactorsand
some300assays.Theresultsshowatradeoffbetweenhowthemethodsperformaccordingtothedifferentcriteria,anda
dichotomy of method types. Algorithms that construct motifs with low information content predict PBM probe ranking
more faithfully, while methods that produce highly informative motifs match reference motifs better. Interestingly, in
predictinghigh-affinitybinding,allmethodsgivefarpoorerresultsforinvivoassayscomparedtoinvitroassays.
Citation:OrensteinY,LinhartC,ShamirR(2012)AssessmentofAlgorithmsforInferringPositionalWeightMatrixMotifsofTranscriptionFactorBindingSites
UsingProteinBindingMicroarrayData.PLoSONE7(9):e46145.doi:10.1371/journal.pone.0046145
Editor:YingXu,UniversityofGeorgia,UnitedStatesofAmerica
ReceivedJuly23,2012;AcceptedAugust27,2012;PublishedSeptember28,2012
Copyright: ? 2012 Orenstein et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited.
Funding:Thisstudywassupportedinpartbythe
您可能关注的文档
- AS03 Adjuvanted AH1N1 Vaccine Associated with an Abrupt Increase in the Incidence of Childhood Narcolepsy in Finland 英文参考文献.doc
- Aseptic Meningitis in Children Analysis of 506 Cases 英文参考文献.doc
- Ascorbic Acid Has Superior Ex Vivo Antiproliferative, Cell Death-Inducing and Immunomodulatory Effects over IFN-α in HTLV-1-Associated Myelopathy 英文参考文献.doc
- Asc1 Supports Cell-Wall Integrity Near Bud Sites by a Pkc1 Independent Mechanism 英文参考文献.doc
- Ascl1 (Mash1) Defines Cells with Long-Term Neurogenic Potential in Subgranular and Subventricular Zones in Adult Mouse Brain 英文参考文献.doc
- Asiatic Acid Inhibits Pro-Angiogenic Effects of VEGF and Human Gliomas in Endothelial Cell Culture Models 英文参考文献.doc
- Ashkenazi Jewish Centenarians Do Not Demonstrate Enrichment in Mitochondrial Haplogroup J 英文参考文献.doc
- Ask A Biologist Bringing Science to the Public 英文参考文献.doc
- Ascorbate Peroxidase from Leishmania major Controls the Virulence of Infective Stage of Promastigotes by Regulating Oxidative Stress 英文参考文献.doc
- Ascl2 Knockdown Results in Tumor Growth Arrest by miRNA-302b-Related Inhibition of Colon Cancer Progenitor Cells 英文参考文献.doc
文档评论(0)