PPT-Gene expression analysis

Author : olivia-moreira | Published Date : 2016-05-08

and transcriptomics Daniel Hurley What are we going to talk about Understanding the core principles and root hypothesis of transcriptomics Choosing between different

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Gene expression analysis: Transcript

and transcriptomics Daniel Hurley What are we going to talk about Understanding the core principles and root hypothesis of transcriptomics Choosing between different technologies How to design an experiment. 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 . 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. 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. 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 . 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. 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. . 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.

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