PPT-Functional Annotation of Animal Genomes (FAANG)

Ravi N Ravindranath PhD Fertility and Infertility Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Is FAANG important for NIH. Fall 2012. C. ommunity . A. ssessment of. C. ommunity . A. nnotation with . O. ntologies. (CACAO). Spring 2010. Fall 2010. Spring 2011. Fall 2011. Institutions. TAMU. TAMU. UCL. TAMU. Miami (Ohio). Archaea. Matthew Blow. mjblow@lbl.gov. Adam . Deutschbauer. Morgan Price. Kelly Wetmore. Adam . Arkin. Cindi. Hoover. Feng. Chen. Jim Bristow. Deutschbauer. lab, LBNL. JGI. G. ene function annotation . :DAVID. D. atabase for . A. nnotation, . V. isualization and . I. ntegrated . D. iscovery . (. DAVID ). Functional Annotation Tool. . Gene Ontology. Protein interaction . Protein domain. Pathway. . AGeS: A Software System for Annotation and Analysis of Genome Sequences . *jaques.reifman@us.army.mil (301) 619-7915 . Kamal Kumar, Valmik Desai, Li Cheng, Maxim Khitrov, Deepak Grover, Ravi Vijaya Satya, Chenggang Yu, Nela Zavaljevski, and . Organelle gene expression processes. Organelle-to-nucleus signaling. (retrograde regulation). PCB6528 Plant Cell and Developmental Biology Spring . 2012. Organelle genomes, gene expression and signaling. ASM-JGI. . 2012. Transferring information to . new genomes. Database. Lists of genes. Known functions of. Homologs or subsets. New knowledge. Curation is rate limiting. Literature. Datasets. Biocurators. Comparative genomics of sponges, sea anemones, and multicellular pancakes. Mansi Srivastava. Rokhsar Lab, Department of Molecular and Cell Biology, UC Berkeley. Reddien Lab, Whitehead Institute for Biomedical Research. Hardison. . Genomics 2_2. 1/7/15. 1. Y Chromosome. 3 billion bp = 3 Gb. Chr1 247 Mb. Chr12 132 Mb. Chr22 50 Mb. A human . genome (. male). The . genome. is . all the DNA. in a cell.. All the DNA on all the chromosomes. Program for today. :. - . Have. all genes . been. . studied. . with. . the. same . intensity. ?. - . Functional. . annotation. . of. genes/. gene. . products. : Gene . Ontology. (GO. ). - . Source:. Editors. Title:. DEL05.x: Annotation tool - Draft requirements study for an annotation tool - Att.1: Presentation. Purpose:. Discussion. Contact:. Marc Lecoultre. E-mail: . ml@mllab.ai . Abstract:. However, genomes are large and complex and visualizing this information is not easy. You need to imagine that the raw annotation information, by itself, can be contained in a text file, which could include positional information (coordinates relative to the reference genome) and different features (e.g. annotation type – gene, mRNA, intron/exon, variant, UTR, etc.). Nikos. . Kyrpides. DOE . Joint Genome institute. Two main goals of genome analysis:. Evolutionary analysis. How does an organism compare to the rest?. Metabolic reconstruction. What can an organism do and how?. Program for today:. - . Functional. . annotation. . of. genes/. gene. . products. : Gene . Ontology. (GO). - . significance. . of. . annotations. : . hypergeometric. . test. - (. mathematical. What . is . Functional. . Genomics?. RNA . Transcription/Gene. . Expression. Measuring Gene. . Expression. Microarrays. High-throughput. . Sequencing. Transcriptional. . Regulation. Transcription.