PPT-Challenges in Microarray Data Analysis

Jagath C Rajapakse Nanyang Technological University InCoB 2009 Singapore Outline Properties of microarray data Clustering and classification Gene selection SVMRFE with MRMR SVTRFE Building gene regulatory networks GRN. Mark . Bergland. and Karen . Klyczek. University of Wisconsin-River Falls. . ACUBE Annual Meeting, Lakeland College, . 2012. Case It! Project. URL for . Case It! Home Page:. http. ://caseit.uwrf.edu. . Differential . expression, clustering, networks, and functional enrichment. STEMREM 201 Fall 2012. Aaron . Newman, Ph.D.. 10/17/12. A . genomics approach . to . biology involves…. A plethora of . Transcriptomics – towards RNASeq Federico M. Giorgi – federico.giorgi@gmail.com Analisi del Genoma e Bioinformatica Corso di Laurea Specialistica in Biotecnologie delle piante KEMRI Wellcome Largest malaria study of its kind made possible by Arrayjet technology www.Arrayjet.com mail@Arrayjet.com Nearly half the world’s population is at risk of Malaria, and the Plasmodiu Microarray . Analysis and Omics Technology. Introduction. Approximately humans have 25000 genes. Only . a fraction of these are actively expressed as mRNAs at any one time. . Hybridization between the cDNA reverse transcribed from a biological sample to a pre-designed complementary DNA probe arranged on a slide, or array, is the basis of DNA microarrays.. - Overview -. Why gene expression analysis?. Quantification of mRNA transcript abundance. High specificity, +/- high through-put. Requires sequence knowledge. Considerations. Experimental question. Species limitations . Transcriptomic. (and other . omic. ) Data Analysis in Bioinformatics. Outline. What is . transcriptome. Basic techniques to obtain . transcriptomic. data. Computational . and statistical methods involved in . Microarray . Analysis and Omics Technology. Introduction. Approximately humans have 25000 genes. Only . a fraction of these are actively expressed as mRNAs at any one time. . Hybridization between the cDNA reverse transcribed from a biological sample to a pre-designed complementary DNA probe arranged on a slide, or array, is the basis of DNA microarrays.. Peptide intensity vs m/z. Previous Lecture: . Proteomics Informatics. Gene Expression Analysis (I). This Lecture. Learning Objectives. Microarray experimental details. Microarray data formats. QC analysis and data exploration. Outline. Introduction. Two review papers. Quality control (. MetaQC. ). Meta-analysis for detecting differentially expressed genes (. MetaDE. ). Meta-analysis for detecting pathways (. MetaPath. ). 1. Introduction. AMB Review 11/2010. Consensus Clustering . (. Monti. et al. 2002). Internal validation method for clustering algorithms.. Stability based technique.. Can be used to compare algorithms or for estimating the number of clusters in the data.. V2: . data imputation . V3: batch effects. What is measured by microarrays?. Microarray normalization. Differential gene expression (DE) analysis based on microarray data. Detection of outliers. RNAseq. Shilpa. . Kaistha. Department of Microbiology. Institute of Biosciences & Biotechnology. CSJM University, Kanpur. Microarrays can be used in many types of experiments including . Genotyping. epigenetics. MBI401-High throughput Data analysis. Mamta Sagar. Department of Bioinformatics. UIET-IBSBT, CSJM University, Kanpur. 1. INTRODUCTION. Functional genomics involves the analysis of large datasets of information derived from various biological experiments. One such type of large-scale experiment involves monitoring the expression levels of thousands of genes simultaneously under a particular condition,.