PPT-V4 – differential gene expression

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. Inducible gene expression. kinetics of . β-galactosidase. enzyme induction. Add inducer. start transcription = mRNA accumulation. mRNA translation = protein accumulation. Remove inducer. Stop. transcription (. 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.. Bing Zhang. Department of Biomedical Informatics. Vanderbilt University. bing.zhang@vanderbilt.edu. Overall workflow of gene expression studies. Microarray. Biological question. Experimental . design. 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. Advances in Gene Expression Science . Allow Scientists to Compare & Contrast . Expression Patterns of two Biological States. Biological State #1. Biological State #2 State. Comparison of Genetic Profiles of Adipose Tissue in Identical Twins . . 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. University of Notre Dame. Kristin Hager, Associate Teaching Professor, Biological Sciences. Joseph O’Tousa, Professor, Biological Sciences. WH Freeman. Marc Mazzoni, Senior Editor, Life Sciences. Elaine Palucki, Editor, Adjunct Assistant Professor Biology, Brooklyn College. 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 Controlling gene expression is often accomplished by controlling transcription initiation.. Regulatory proteins . bind to DNA to either block or stimulate transcription, depending on how they interact with RNA polymerase.. Drosophila. Embryos using . lacZ. Transgenes. June 18. th. ABLE 2014. University of Oregon, Eugene. Cathy Silver Key. Julie Gates. Jessica Sawyer. Kirsten . Guss. Acknowledgements. Funding from . Roberta . 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. . Venet. , et al.. PLoS. Computational Biology, 2011. Molly Carroll. Biomedical Research Methods. Characterize mechanism in the model. Derive a marker that changes when the mechanism is altered. Show .