PPT-Motif Enrichment Analysis in Co-Expressed Gene Sets and Hig

Wyeth Wasserman Jan 18 2012 opossumcisregcaoPOSSUM3 Welcome If you encounter any technical difficulties during the webinar Type a report using the chat option Slide presentation 20 min Compile Questions as they are submitted and answer them during the final QampAdiscussion period. Simon Andrews. simon.andrews@babraham.ac.uk. @. simon_andrews. v. 1.0. 1. Rationale. 2. Gene A. Gene B. Gene C. Hit A. Hit B. Hit C. Prom A. Prom B. Prom C. GGATCC. GGATCC. GGATCC. Basic Questions. Does the sequence around my hits look unusual?. Group . (. A). rabidopsis. :. David Nieuwenhuijse. Matthew Price. Qianqian Zhang. Thijs Slijkhuis. Species:. C. . Elegans. Project:. . Advanced (+Basic). Progress Report. Project Overview. Results so far. Ph. D. .. Affymetrix. . Probeset. Mapping and . Medicago. Genome Annotation (Mt4.0 RC1). About . Affymetrix. . Medicago. . GeneChip. Mapping . Algorithm and Tool. Bioinformatics . Resources . for . 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 . Analysis. :. Aaron Brooks. & . Fang Yin Lo. 8/21/2012. Introduction to Systems Biology 2012. making sense of big data. Mischel. et al, 2004. Experimental . Design. Data . collection. Data . analysis. Alignment.. Model parameters from neutral sequence. Estimation example. Estimation example 2. HMM version. Protein Coding Gene. Known. non-. coding gene: . XIST. ch10. chX. RepA. Different gene conservation patterns. Saccharomyces . cerevisiae. .. Group . Populus. :. Petra van Berkel. Casper Gerritsen. Astri. . Herlino. Brian Lavrijssen. Dataset of . S. . cerevisiae. Data generated by . Nookaew. . et al . (2012). NOVA’s . A . Tale of Two Mice. : Chapter 1. Nucleotide. (consists of a base, . a 5-carbon sugar, . and a phosphate group). Hydrogen. Bonds . (. between . bases). Phosphodiester. Bond. . (between adjacent nucleotides). simon.andrews@babraham.ac.uk. @. simon_andrews. v. 1.0. 1. Rationale. 2. Gene A. Gene B. Gene C. Hit A. Hit B. Hit C. Prom A. Prom B. Prom C. GGATCC. GGATCC. GGATCC. Basic Questions. Does the sequence around my hits look unusual?. Vladimir Teif. BS222 – Genome Science Lecture 9. Module structure. Genomes, sequencing projects and genomic databases (VT) (Oct 9, 2018). Sequencing technologies (VT) (Oct 11, 2018). Genome architecture I: protein coding genes (VT) (Oct 16, 2018). and RNA-. seq. Vladimir Teif. Intro to NGS analysis. Proficio. course 2020. NGS data integration. http://determinedtosee.com/wp-content/uploads/2014/08/jigsaw-puzzle.jpg. 1. Signal + existing annotation. Network motifs. Network clusters / modules. Co-clustering networks & expression. Network comparison. (species, conditions). Integration of genetic & physical nets. Network visualization. Network. 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 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.:.