PPT-Differential Expression Analysis

Introduction to Systems Biology Course Chris Plaisier Institute for Systems Biology Glioma A Deadly Brain Cancer Wikimedia commons miRNAs in Cancer Caldas et al 2005 RISC Utility of miRNAs in Cancer. limma. package. 20 March 2012. Functional Genomics. Linear regression. Fit a straight line through a set of points such that the distance from the points to the line is minimized. The slope of the line is adjusted to minimize the . Ju. . Han Kim . Division of Biomedical Informatics, Seoul National University College of Medicine, Seoul, Korea, . Presenter: Zhen Gao . 2. Outline. Review of major computational . approaches to facilitate biological interpretation of . Bing Zhang. Department of Biomedical Informatics. Vanderbilt University. bing.zhang@vanderbilt.edu. Overall workflow of gene expression studies. Microarray. Biological question. Experimental . design. Jenny . Wu. Outline. Goals : Practical guide to NGS data processing. Bioinformatics in NGS data analysis. Basics: terminology, data formats, general workflow etc.. Data Analysis Pipeline. Sequence QC and preprocessing. . 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 . A paper by: Paul Kocher, Joshua Jaffe, and Benjamin Jun. Presentation by: Michelle Dickson. Power Analysis. Introduction. Simple Power Analysis (SPA). Theory. Experimental Results. Prevention. Differential Power Analysis (DPA). Prokaryotes and eukaryotes precisely regulate gene expression in response to environmental conditions. In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types. Moni. Naor. Weizmann Institute of Science. The Brussels Privacy . Symposium. November 8. th. 2016. What is Differential Privacy. Differential Privacy is a concept . Motivation. Rigorous mathematical definition. analysis - outliers. V2: batch effects. V3: data imputation. What . is measured by microarrays?. Microarray normalization. Differential gene expression (DE) analysis based on microarray data. Detection of outliers. Ron Shamir. School of Computer Science. Tel Aviv University. April 2013. 1. Sources: . Igor Ulitsky and Ron Shamir. Identification of Functional Modules using Network Topology and High-Throughput Data. BMC Systems Biology 1:8 (2007). . Resources and Gene Set Enrichment Analysis. Genomics Lesson . 8_3. Hardison. resources. 3/24/15. 2. Try it yourself. Go to Gene Expression Omnibus at NCBI. http://. www.ncbi.nlm.nih.gov. /geo/. Choose a dataset of interest, e.g.:. What is measured by microarrays?. Microarray normalization. Differential gene expression (DE) analysis based on microarray data. Detection of outliers. RNAseq. data. DE analysis based on . RNAseq. data. RNA-Seq. G-OnRamp Beta Users Workshop. Wilson Leung. 07/2017. Outline. Design considerations for RNA-Seq experiments. Interpret FastQC results. Optimize alignment parameters for HISAT. Assess alignment statistics with CollectRnaSeqMetrics. 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.