PPT-V3 – differential gene expression analysis

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. 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. Alisha Holloway, PhD. Gladstone Bioinformatics Core Director. What is RNA-seq?. Use of high-throughput sequencing technologies to assess the RNA content of a sample.. Why do an RNA-seq experiment?. Detect . . 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 . Draw 8 boxes on your paper. Gene regulation accounts for some of the phenotypic differences between organisms with similar genes.. 2005-2006. Gene regulation in bacteria. Control of gene expression enables individual bacteria to adjust their metabolism to environmental change. Identification of a Differentially-expressed Gene in Fatty Liver Acta Biochim Biophys SinVol. 39, No. 9 and 5 females in each group). All of the geese were hatchedconditions. All of the geese had f 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. transcriptomic. ) . data analysis. Ståle. . Nygård. , Bioinformatics core facility, OUS/UiO. staaln@ifi.uio.no. Gene expression. Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product.. Systematic . In . silico. . analysis using public database. Sung Hwan Lee. 1,4. , Baek Gil . Kim. 2,3. , . Ho Kyoung Hwang. 1,4. , Woo . Jung . Lee. 1,4. , Chang . Moo Kang. 1,4**.  . 1. Department . 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.:. Dr. Xiangyu Li. KTH-Royal In. stitute. of Technology. http://sysmedicine.com. 1. Where the transcripts come from?. 2. Pre-mRNA. Intron. Patterns . of alternative . splicing. 3. HPA 37 different human tissues. 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.