Methods of microarray data analysis V : [5th international conference for the Critical Assessment of Microarray Data Analysis (CAMDA), November 10-12 2004, Durham, North Carolina, USA

Since the inception of microarrays, studies in this field have drastically evolved with analysis methods needing to advance in-step. The CAMDA conference plays a role in this ever-changing discipline by providing a forum in which investigators can analyze the same datasets using different methods. **Methods of Microarray Data Analysis V** is the fifth book in this series, and focuses on the important issue of analyzing array data in a time series with correlating biological data. Previous books in this series focused on classification (Volume I), pattern recognition (Volume II), quality control issues (Volume III), and survival analysis (Volume IV). In this volume, all investigators analyzed a single dataset on the lifecycle of the most deadly of malaria parasites, Plasmodium falciparum. The emphasis this year is on the application of novel and existing computational methodologies towards infectious disease. We highlight an introductory chapter by Raphael D. Isokpehi, a leading expert in the field of malaria. Ten of the papers presented at the conference are included, which range from the inference of genetic networks to the analysis of the spatial correlation of array data. This book is an excellent reference for academic and industrial researchers who want to keep abreast of the state-of-the-art in microarray data analysis. Patrick McConnell is a researcher in the Duke Bioinformatics Group in the Duke Comprehensive Cancer Center. Simon M. Lin is a faculty member in the Robert H. Lurie Comprehensive Cancer Center and associate director of Bioinformatics at Northwestern University. Patrick Hurban is director of Investigational Genomics at Icoria, Inc., a Clinical Data company. Front Matter....Pages i-xiii Data Mining of Malaria Parasite Gene Expression for Possible Translational Research....Pages 1-10 Constructing Probabilistic Genetic Networks of Plasmodium falciparum from Dynamical Expression Signals of the Intraerythrocytic Development Cycle....Pages 11-26 Simple Methods for Peak and Valley Detection in Time Series Microarray Data....Pages 27-44 Oxidative Stress Genes in Plasmodium falciparum as Indicated by Temporal Gene Expression....Pages 45-58 Identifying Stage-Specific Genes by Combining Information from Two Different Types of Oligonucleotide Arrays....Pages 59-74 Construction of Malaria Gene Expression Network Using Partial Correlations....Pages 75-88 Detecting Network Motifs in Gene Co-expression Networks Through Integration of Protein Domain Information....Pages 89-102 Chromosomal Clustering of Periodically Expressed Genes in Plasmodium falciparum ....Pages 103-119 PlasmoTFBM: An Intelligent Queriable Database for Predicted Transcription Factor Binding Motifs in Plasmodium falciparum ....Pages 121-136 Linking Gene Expression Patterns and Transcriptional Regulation in Plasmodium falciparum ....Pages 137-156 Chromosomal Spatial Correlation of Gene Expression in Plasmodium falciparum ....Pages 157-171 Back Matter....Pages 173-175 As studies using microarray technology have evolved, so have the data analysis methods used to analyze these experiments. The CAMDA (Critical Assessment of Microarray Data Analysis) conference was the first to establish a forum for a cross section of researchers to look at a common data set and apply innovative analytical techniques to microarray data. "Methods of Microarray Analysis V" includes selected papers from CAMDA'04, and focuses on data sets relating to a significant global health issue, malaria. Previous books focused on classification (Volume I), pattern recognition (Volume II), quality control issues (Volume III), and associating array data with a survival endpoint, lung cancer, (Volume IV). The contributions come from research fields including statistics, biology, computer science and mathematics. Part of the book is devoted to review papers, which provide a more general look at various analytical approaches. It also presents some background readings for the advanced topics discussed in the CAMDA papers This book is dedicated solely to the analysis of microarray data. Its unique approach of presenting different methods by analyzing the same data set shows the strengths and weakness of each method. Part of the book is devoted to review papers, which provide a more general look at various analytical approaches. It also presents some background readings for the advanced topics discussed in the CAMDA papers.