目录 前言 v 撰稿人 ix 第一部分：相互作用 1. 用Linguamatics公司研发的I2E软件从发表的文献中挖掘蛋白质相互作用 3 Judith B and y，David Milward，and Sarah McQuay 2. 基因组规模实验中转录因子与DNA结合的相对亲和力、特异性和敏感度 15 Vladimir A.Kuznetsov 3. 抑制因子-靶标数据的管理：步骤和在途径分析上的作用 51 Sreenivas Devidas 4. 用功能蛋白质芯片描绘蛋白质相互作用网络 63 Dawn R.Mattoon and Barry Schweitzer 5. 蛋白质相互作用的手工注释 75 Svetlana Bureeva，Svetlana Zvereva，Valentin Romanov， and Tatiana Serebryiskaya 第二部分：分析 6. 基因集富集分析 99 Charles A.Tilford and NathanO.Siemers 7. PANTHER途径：一个整合了数据分析工具且基于本体的途径数据库 123 HuaiyuMi and PaulThomas 8. 采用网络分析优化排序影响途径的基因 141 AaronN.Chang 9. 从多样的功能基因组数据中发掘生物学网络 157 Chad L.Myers，Camelia Chiriac， and Olga G.Troyanskaya 10. 在基于知识的集成平台上对组学数据及小分子化合物的函数分析 177 Yuri Nikolsky，Eugene Kirillov，Roman Zuev，Eugene Rakhmatulin， and Tatiana Nikolskaya 11. 动力学模型作为一种整合多层次动态实验数据的工具 197 Ekaterina Mogilevskaya，Natalia Bagrova，Tatiana Plyusnina，Nail Gizzatkulov，Eugeniy Metelkin，Ekaterina Goryacheva，Sergey Smirnov，Yuriy Kosinsky，Aleks and er Dorodnov，Kirill Peskov，Tatiana Karelina，Igor Goryanin， and OlegDemin 12. Cytoscape：用于网络建模的一个基于社区的框架 219 Sarah Killcoyne，Gregory W.Carter，Jennifer Smith，and John Boyle 13. 用语义数据集成和知识管理表示生物网络相关性 241 Sascha Losko and Klaus Heumann 14. 复杂的、多数据类型及多工具分析的解决方案：运用工作流程与流水线方法的 原则及应用 259 Robin E.J.Munro and YikeGuo 第三部分：应用 15. 高通量siRNA筛选结合化合物筛选作为一种干扰生物系统以及识别目标途径的方法 275 Jeff Kiefer，Hongwei H.Yin，QiangQ.Que， and Spyro Mousses 16. 用高密度等位基因关联数据进行途径和网络的分析 289 Ali Torkamani and Nicholas J.Schork 17. miRNAs：从生物起源到网络 303 Giuseppe Russo and Antonio Giordano 18. MetaMiner(CF)：疾病导向的生物信息学分析环境 353 Jerry M.Wright，Yuri Nikolsky，Tatiana Serebryiskaya， and Diana R.Wetmore 19. 转化研究与生物医学信息学 369 Michael Liebman 20. ArrayTrack：一个美国食品及药物管理局(FDA)和公共基因组工具 379 Hong Fang，StephenC.Harris，Zhenjiang Su，Minjun Chen，Feng Qian，Leming Shi，RogerPerkins， and Weida Tong 索引 399 (高友鹤 尹剑锐 译) Contents Preface v Contributors ix SECTION I：INTERACTIONS 1. Mining Protein–Protein Interactions from Published Literature Using Linguamatics I2E 3 Judith B and y，David Milward， and Sarah McQuay 2. Relative Avidity，Specificity， and Sensitivity of Transcription Factor–DNA Binding in Genome-Scale Experiments 15 Vladimir A. Kuznetsov 3. Curation of Inhibitor-Target Data：Process and Impact on Pathway Analysis 51 Sreenivas Devidas 4. Profiling Protein Interaction Networks with Functional Protein Microarrays 63 Dawn R. Mattoon and Barry Schweitzer 5. Manual Annotation of Protein Interactions 75 Svetlana Bureeva，Svetlana Zvereva，Valentin Romanov， and Tatiana Serebryiskaya SECTION II：ANALYSIS 6. Gene Set Enrichment Analysis 99 Charles A. Tilford and Nathan O. Siemers 7. PANTHER Pathway：An Ontology-Based Pathway Database Coupled with Data Analysis Tools 123 Huaiyu Mi and Paul Thomas 8. Prioritizing Genes for Pathway Impact Using Network Analysis 141 Aaron N. Chang 9. Discovering Biological Networks from Diverse Functional Genomic Data 157 Chad L. Myers，Camelia Chiriac， and Olga G. Troyanskaya 10. Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated “Knowledge-Based” Platform 177 Yuri Nikolsky，Eugene Kirillov，Roman Zuev，Eugene Rakhmatulin， and Tatiana Nikolskaya 11. Kinetic Modeling as a Tool to Integrate Multilevel Dynamic Experimental Data 197 Ekaterina Mogilevskaya，Natalia Bagrova，Tatiana Plyusnina，Nail Gizzatkulov，Eugeniy Metelkin，Ekaterina Goryacheva，Sergey Smirnov，Yuriy Kosinsky，Aleks and er Dorodnov，Kirill Peskov，Tatiana Karelina，Igor Goryanin， and Oleg Demin 12. Cytoscape：A Community-Based Framework for Network Modeling 219 Sarah Killcoyne，Gregory W. Carter，Jennifer Smith， and John Boyle 13. Semantic Data Integration and Knowledge Management to Represent Biological Network Associations 241 Sascha Losko and Klaus Heumann 14. Solutions for Complex，Multi Data Type and Multi Tool Analysis：Principles and Applications of Using Workflow and Pipelining Methods 259 Robin E. J. Munro and Yike Guo SECTION III：APPLICATIONS 15. High-Throughput siRNA Screening as a Method of Perturbation of Biological Systems and Identification of Targeted Pathways Coupled with Compound Screening 275 Jeff Kiefer，Hongwei H. Yin，Qiang Q. Que， and Spyro Mousses 16. Pathway and Network Analysis with High-Density Allelic Association Data 289 Ali Torkamani and Nicholas J. Schork 17. miRNAs：From Biogenesis to Networks 303 Giuseppe Russo and Antonio Giordano 18. MetaMiner (CF)：A Disease-Oriented Bioinformatics Analysis Environment 353 Jerry M. Wright，Yuri Nikolsky，Tatiana Serebryiskaya， and Diana R. Wetmore 19. Translational Research and Biomedical Informatics 369 Michael Liebman 20. ArrayTrack：An FDA and Public Genomic Tool 379 Hong Fang，Stephen C.Harris，Zhenjiang Su，Minjun Chen，Feng Qian，Leming Shi，Roger Perkins， and Weida Tong Index 399
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