PPT-Differential Gene Expression with the

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 . The problem to be solved (an example). Hauf, J., Zimmermann, F.K., M. ü. ller, S., 2000. Simultaneous genomic over expression of seven glycolytic enzymes in the yeast Saccharomyces cerevisiae. Ezyme. Microbiol. Technol.. FREQUENCY 10k 69 72 75 78 81 84 87 90 GAIN TA01b 100k 1M 10M 100M 1G 60 63 66 Pseudo-Differential Differential)/95dB (Pseudo-Differential)Programmable Compression VoltagesOnboard Reference Reference Vibrio cholerae . HHMI 2011. Sara Fassio. Dr. Claudia H. ä. se. Dr. Yusuke Minato . Cholera. Infection of small intestine . Causes severe diarrhea and electrolyte loss. 3-5 million cases a year. 100,000- 120,000 deaths per year . Stephen Montgomery. smontgom@stanford.edu. montgomerylab.stanford.edu. @. sbmontgom. Identifying the genes and variants responsible for disease.. Monogenic to polygenic diseases. Rare to common variants. . 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 . Group. : Mohamed . Hairi. Bin Abdul . Shukur. (01DAD10F2060). . Khairil. . Azreen. Bin . Kholid. (01DAD10F2046). Amir Yusuf Bin . Hazimi. (01DAD10F2058). Muhammad . Amin. TUMOR SUPRESSOR PROTEINS. ATP. ENZYMES THAT CONTROL CELLULAR RESPIRATION. ADAPTIVE GENE PRODUCTS ARE ONLY REQUIRED UNDER CERTAIN CONDITIONS. GENES FOR PROTEIN DIGESTION ARE TURNED OFF WHEN THERE IS NO PROTEIN AVAILABLE. . 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 We performed a genome-wide analysis of gene expressionto identify germline- and sex-regulated genes.Using mutants that cause defects in germ cell proliferationor gametogenesis, we identiÞed sets of g  which is designed to allow . expression.  (. transcription.  and . translation. ) of the inserted section of . DNA. . The . vector.  carries a . promoter.  (normally inducible) on one side of the . Pearley Chinta and Juliet V. Spencer . Abstract. Methods. Results. Conclusions. HCMV is a widespread pathogen in the general population and can cause severe disease in immune-compromised hosts. HCMV manipulates immune responses in several ways, one of which includes encoding genes with homology to host chemokine receptors. HCMV US27 encodes a chemokine-like receptor that stimulates host gene expression. While, no chemokine ligand has been identified for US27, it is constitutively active. US27 stimulates the gene expression of antioxidant response element (ARE) regulated genes by activation of the transcription factor nuclear respiratory factor 1 (NRF-1). The goal of this project is to identify specific host and viral genes that are regulated by US27. Increased expression of antioxidant genes is likely to benefit virus infection and enable more progeny virus to be produced. Thus, a better understanding of the US27 function has the potential to lead to the development of novel antiviral therapies necessary to treat HCMV infection. . 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.