* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Harrisslides
No-SCAR (Scarless Cas9 Assisted Recombineering) Genome Editing wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
Non-coding DNA wikipedia , lookup
Nutriepigenomics wikipedia , lookup
Metagenomics wikipedia , lookup
Whole genome sequencing wikipedia , lookup
Gene therapy of the human retina wikipedia , lookup
Human genetic variation wikipedia , lookup
Human genome wikipedia , lookup
Genetic engineering wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Genomic library wikipedia , lookup
Genome (book) wikipedia , lookup
Mir-92 microRNA precursor family wikipedia , lookup
Gene expression profiling wikipedia , lookup
Gene expression programming wikipedia , lookup
History of genetic engineering wikipedia , lookup
Designer baby wikipedia , lookup
Helitron (biology) wikipedia , lookup
Microevolution wikipedia , lookup
Human Genome Project wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Pathogenomics wikipedia , lookup
Public health genomics wikipedia , lookup
Genome editing wikipedia , lookup
Genome evolution wikipedia , lookup
Using The Gene Ontology: Gene Product Annotation GO Project Goals • Compile structured vocabularies describing aspects of molecular biology • Describe gene products using vocabulary terms (annotation) • Develop tools: • to query and modify the vocabularies and annotations • annotation tools for curators GO Data GO provides two bodies of data: • Terms with definitions and crossreferences • Gene product annotations with supporting data The Three Ontologies •Molecular Function — elemental activity or task nuclease, DNA binding, transcription factor •Biological Process — broad objective or goal mitosis, signal transduction, metabolism •Cellular Component — location or complex nucleus, ribosome, origin recognition complex DAG Structure Directed acyclic graph: each child may have one or more parents The True Path Rule Every path from a node back to the root must be biologically accurate GO Annotation • Association between gene product and applicable GO terms • Provided by member databases • Made by manual or automated methods DAG Structure Annotate to any level within DAG DAG Structure mitotic chromosome condensation S.c. BRN1, D.m. barren Annotate to any level within DAG DAG Structure mitosis S.c. NNF1 mitotic chromosome condensation S.c. BRN1, D.m. barren Annotate to any level within DAG GO Annotation: Data • Database object: gene or gene product • GO term ID • Reference • publication or computational method • Evidence supporting annotation GO Evidence Codes IDA - Inferred from Direct Assay IMP - Inferred from Mutant Phenotype TAS - Traceable Author Statement NAS - Non-traceable Author Statement IGI - Inferred from Genetic Interaction IC - Inferred by Curator IPI - Inferred from Physical Interaction ISS - Inferred from Sequence or structural Similarity IEP - Inferred from Expression Pattern IEA - Inferred from Electronic Annotation ND - Not Determined GO Evidence Codes IDA - Inferred from Direct Assay IMP - Inferred from Mutant Phenotype TAS - Traceable Author Statement NAS - Non-traceable Author Statement IGI - Inferred from Genetic Interaction IC - Inferred by Curator IPI - Inferred from Physical Interaction ISS - Inferred from Sequence or structural Similarity IEP - Inferred from Expression Pattern IEA - Inferred from Electronic Annotation ND - Not Determined From primary literature GO Evidence Codes From reviews or introductions IDA - Inferred from Direct Assay IMP - Inferred from Mutant Phenotype TAS - Traceable Author Statement NAS - Non-traceable Author Statement IGI - Inferred from Genetic Interaction IC - Inferred by Curator IPI - Inferred from Physical Interaction ISS - Inferred from Sequence or structural Similarity IEP - Inferred from Expression Pattern IEA - Inferred from Electronic Annotation ND - Not Determined From primary literature GO Evidence Codes From reviews or introductions IDA - Inferred from Direct Assay IMP - Inferred from Mutant Phenotype TAS - Traceable Author Statement NAS - Non-traceable Author Statement IGI - Inferred from Genetic Interaction IC - Inferred by Curator IPI - Inferred from Physical Interaction ISS - Inferred from Sequence or structural Similarity IEP - Inferred from Expression Pattern IEA - Inferred from Electronic Annotation ND - Not Determined From primary literature GO Evidence Codes From reviews or introductions IDA - Inferred from Direct Assay IMP - Inferred from Mutant Phenotype TAS - Traceable Author Statement NAS - Non-traceable Author Statement IGI - Inferred from Genetic Interaction IC - Inferred by Curator IPI - Inferred from Physical Interaction ISS - Inferred from Sequence or structural Similarity IEP - Inferred from Expression Pattern IEA - Inferred from Electronic Annotation ND - Not Determined From primary literature automated GO Annotation: Methods • Manual • Automated • sequence similarity • transitive annotation • nomenclature, other text matching Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C Encodes Saccharomyces cerevisiae Purine Nucleoside Phosphorylase. J. Bacteriology 183(16): 4910-4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol. 183(16): 4910–4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol. 183(16): 4910–4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA FUNCTION: purine nucleoside phosphorylase Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C ncodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol. 183(16): 4910–4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA IMP FUNCTION: purine nucleoside phosphorylase Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol. 183(16): 4910–4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA IMP FUNCTION: purine nucleoside phosphorylase Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol. 183(16): 4910–4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA FUNCTION: purine nucleoside phosphorylase PROCESS: IMP purine nucleoside catabolism Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol. 183(16): 4910–4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA FUNCTION: purine nucleoside phosphorylase PROCESS: IMP This paper has no data for cellular component. purine nucleoside catabolism Automated Annotation: InterPro Example YFP InterPro entry GO entry InterPro2go links InterPro entries and GO terms Automated Annotation: InterPro Example Run InterProScan to link YFP and InterPro entry InterPro entry YFP GO entry InterPro2go links InterPro entries and GO terms Automated Annotation: InterPro Example Run InterProScan to link YFP and InterPro entry InterPro entry YFP Infer GO term from the other two links GO entry InterPro2go links InterPro entries and GO terms AmiGO Browser detailed view of term AmiGO Browser gene products annotated to term GO Annotation: Contributors • • • • • FlyBase Saccharomyces Genome Database Mouse Genome Informatics The Arabidopsis Information Resource Swiss-Prot/TrEMBL/InterPro • WormBase • DictyBase • Gramene • Compugen, Inc. • Pathogen Sequencing Unit (Sanger Institute) • PomBase (Sanger Institute) • Rat Genome Database • The Institute for Genomic Research GO Annotation: Organisms • Fruit fly (Drosophila melanogaster) • Budding yeast (Saccharomyces cerevisiae) • Fission yeast (Schizosaccharomyces pombe) • Human (Homo sapiens) • Mouse (Mus musculus) • Rice (Oryza sativa) • Rat (Rattus norvegicus) • Tsetse fly (G. morsitans) • Caenorhabditis elegans • Arabidopsis thaliana • Vibrio cholerae • Dictyostelium discoideum Current GO Annotations www.geneontology.org • • • • • FlyBase & Berkeley Drosophila Genome Project Saccharomyces Genome Database Mouse Genome Informatics The Arabidopsis Information Resource Swiss-Prot/TrEMBL/InterPro • • • • WormBase DictyBase Gramene Compugen, Inc. • Pathogen Sequencing Unit (Sanger Institute) • PomBase (Sanger Institute) • Rat Genome Database • Genome Knowledge Base (CSHL) • The Institute for Genomic Research The Gene Ontology Consortium is supported by NHGRI grant HG02273 (R01). The Gene Ontology project thanks AstraZeneca for financial support. The Stanford group acknowledges a gift from Incyte Genomics. Conference: Standards and Ontologies for Functional Genomics (SOFG) Towards unified ontologies for describing biology and biomedicine 17 – 20 November 2002 Hinxton Hall Conference Centre Hinxton, Cambridge, UK www.wellcome.ac.uk/hinxton/sofg