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Data Analysis and Visualization in Genomics and Proteomics最新文献

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Integrated Approaches for Bioinformatic Data Analysis and Visualization - Challenges, Opportunities and New Solutions 生物信息学数据分析和可视化的综合方法——挑战、机遇和新的解决方案
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH9
S. Pettifer, J. Sinnott, T. Attwood
{"title":"Integrated Approaches for Bioinformatic Data Analysis and Visualization - Challenges, Opportunities and New Solutions","authors":"S. Pettifer, J. Sinnott, T. Attwood","doi":"10.1002/0470094419.CH9","DOIUrl":"https://doi.org/10.1002/0470094419.CH9","url":null,"abstract":"","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133184933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Data and Predictive Model Integration: An Overview of Key Concepts, Problems and Solutions 数据和预测模型集成:关键概念、问题和解决方案概述
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH3
F. Azuaje, J. Dopazo, Haiying Wang
{"title":"Data and Predictive Model Integration: An Overview of Key Concepts, Problems and Solutions","authors":"F. Azuaje, J. Dopazo, Haiying Wang","doi":"10.1002/0470094419.CH3","DOIUrl":"https://doi.org/10.1002/0470094419.CH3","url":null,"abstract":"This chapter overviews the combination of different data sources and techniques for improving functional prediction. Key concepts, requirements and approaches are introduced. It discusses two main strategies: a) Integrative data analysis and visualisation approaches with an emphasis on the processing of multiple data types or resources; and b) integrative data analysis and visualisation approaches with an emphasis on the combination of multiple predictive models and analysis techniques. It also illustrates problems in which both methodologies can be successfully applied.","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129609111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The C. elegans Interactome: Its Generation and Visualization 秀丽隐杆线虫相互作用组的生成与可视化
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH8
Alban Chesnau, C. Sardet
{"title":"The C. elegans Interactome: Its Generation and Visualization","authors":"Alban Chesnau, C. Sardet","doi":"10.1002/0470094419.CH8","DOIUrl":"https://doi.org/10.1002/0470094419.CH8","url":null,"abstract":"","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125194565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Supervised Methods with Genomic Data: a Review and Cautionary View 基因组数据的监督方法:回顾和警示观点
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH12
R. Díaz-Uriarte
{"title":"Supervised Methods with Genomic Data: a Review and Cautionary View","authors":"R. Díaz-Uriarte","doi":"10.1002/0470094419.CH12","DOIUrl":"https://doi.org/10.1002/0470094419.CH12","url":null,"abstract":"We review well accepted methods to address questions about differential expression of genes and class prediction from gene expression data. We highlight some new topics that deserve more attention: testing of differential expression of specific groups of genes, intra-group heterogeneity and class prediction, gene interaction in predictors, visualisation, difficulties in the biological interpretation of predictor genes and molecular signatures, and the use of ROC[Receiver Operating Characteristic curve]-based statistics for evaluating predictors and differential expression. We end with a review of some serious problems that can limit the potential of these methods; we focus specially on inadequate assessment of the performance of new methods (due to inadequate estimation of error rates and to the use of few and “easy” data sets) and failure to recognise observational studies and include needed covariates. A final comment is made about the need for freely available source code.","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128858573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 30
Integration of Genomic and Phenotypic Data 基因组和表型数据的整合
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH6
A. Clare
{"title":"Integration of Genomic and Phenotypic Data","authors":"A. Clare","doi":"10.1002/0470094419.CH6","DOIUrl":"https://doi.org/10.1002/0470094419.CH6","url":null,"abstract":"Clare, A. (2005) Integration of genomic and phenotypic data. In Data Analysis and Visualization in Genomics and Proteomics, Eds. Francisco Azuaje and Joaquin Dopazo, Wiley, London. ISBN: 0-470-09439-7","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"81 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129365877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
A Guide to the Literature on Inferring Genetic Networks by Probabilistic Graphical Models 用概率图模型推断遗传网络的文献指南
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH13
P. Larrañaga, Iñaki Inza, J. L. Flores
{"title":"A Guide to the Literature on Inferring Genetic Networks by Probabilistic Graphical Models","authors":"P. Larrañaga, Iñaki Inza, J. L. Flores","doi":"10.1002/0470094419.CH13","DOIUrl":"https://doi.org/10.1002/0470094419.CH13","url":null,"abstract":"","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126385191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Advances in Cluster Analysis of Microarray Data 微阵列数据聚类分析研究进展
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH10
Qizheng Sheng, Y. Moreau, F. Smet, K. Marchal, B. Moor
{"title":"Advances in Cluster Analysis of Microarray Data","authors":"Qizheng Sheng, Y. Moreau, F. Smet, K. Marchal, B. Moor","doi":"10.1002/0470094419.CH10","DOIUrl":"https://doi.org/10.1002/0470094419.CH10","url":null,"abstract":"Clustering genes into biological meaningful groups according to their pattern of expression is a main technique of microarray data analysis, based on the assumption that similarity in gene expression implies some form of regulatory or functional similarity. We give an overview of various clustering techniques, including conventional clustering methods (such as hierarchical clustering, k-means clustering, and self-organizing maps), as well as several clustering methods specifically developed for gene expression analysis.","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125636598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 15
Integrative Models for the Prediction and Understanding of Protein Structure Patterns 预测和理解蛋白质结构模式的综合模型
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH14
I. Jonassen
{"title":"Integrative Models for the Prediction and Understanding of Protein Structure Patterns","authors":"I. Jonassen","doi":"10.1002/0470094419.CH14","DOIUrl":"https://doi.org/10.1002/0470094419.CH14","url":null,"abstract":"","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121086993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis 整合基因组特征和蛋白质相互作用网络分析的蛋白质相互作用预测
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH5
L. Lu, Yu Xia, Haiyuan Yu, Alexander Rives, Haoxin Lu, Falk Schubert, M. Gerstein
{"title":"Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis","authors":"L. Lu, Yu Xia, Haiyuan Yu, Alexander Rives, Haoxin Lu, Falk Schubert, M. Gerstein","doi":"10.1002/0470094419.CH5","DOIUrl":"https://doi.org/10.1002/0470094419.CH5","url":null,"abstract":"The recent explosion of genomic-scale protein interaction screens has made it possible to study protein interactions on a level of interactome and networks. In this chapter, we begin with an introduction of a novel approach that probabilistically combines multiple information sources to predict protein interactions in yeast. Specifically, Section 5.2 describes the sources of genomic features. Section 5.3 provides a basic tutorial on machine-learning approaches and","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132086587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Biological Databases: Infrastructure, Content and Integration 生物数据库:基础设施、内容和集成
Data Analysis and Visualization in Genomics and Proteomics Pub Date : 2005-06-15 DOI: 10.1002/0470094419.CH2
Allyson Williams, P. Kersey, Manuela Pruess, R. Apweiler
{"title":"Biological Databases: Infrastructure, Content and Integration","authors":"Allyson Williams, P. Kersey, Manuela Pruess, R. Apweiler","doi":"10.1002/0470094419.CH2","DOIUrl":"https://doi.org/10.1002/0470094419.CH2","url":null,"abstract":"","PeriodicalId":268206,"journal":{"name":"Data Analysis and Visualization in Genomics and Proteomics","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131250394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
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