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TAIR Presentation ASPB 2017
- 1. Supported by individual, institutional, government and corporate subscribers. Thank you all! Eva Huala Tanya Berardini Donghui Li Trilok Prithvi Leonore Reiser Shabari Subramaniam Qian Li Andrey Vetushko Karen Melzer Emily Strait Matt Sousae Ankit Jain The Arabidopsis Information Resource: A curated reference resource for translational plant biology ASPB 2017
- 2. • Manual, literature based annotation – Gene Ontology for biological process, cellular component and molecular function – Plant Ontology for expression and localization – Gene symbols, gene summaries, genes linked to papers – Alleles and Phenotypes • Biocurators with expertise in plant biology – Mostly TAIR but also UniProt,TIGR, BioGrid • Community members-851 individuals (partnership with 17 journals) ‘Gold Standard’ Functional Annotation
- 3. Experimental GO Annotations for Plants GOC 6/12/2017
- 4. • Assign and compare gene functions – Infer function of an unknown gene(s) – Examine evolution of gene function within and across species – Transfer whole genome annotations based on orthology or sequence similarity methods (e.g. Ensembl Compara) • Classify sets of genes/gene lists – GO Functional Categorization – GO Term Enrichment How is this useful?
- 5. SNP Discovery and Genetic Variation of Candidate Genes Relevant to Heat Tolerance and Agronomic Traits in Natural Populations of Sand Rice (Agriophyllum squarrosum) http://journal.frontiersin.org/article/10.3389/fpls.2017.00536/full Identified and sequenced SNP variants Generated UniGene Sets -> BLAST against Arabidopsis -> Candidate genes What is known about these gene(s)? What is the significance/biological effect of the observed variation? Sand rice : drought tolerant potential alternative crop, non model plant What genes contribute to stress tolerance? Search TAIR by name (AT1G32330) or sequence similarity (e.g. BLAST)
- 6. SNP Discovery and Genetic Variation of Candidate Genes Relevant to Heat Tolerance and Agronomic Traits in Natural Populations of Sand Rice (Agriophyllum squarrosum) http://journal.frontiersin.org/article/10.3389/fpls.2017.00536/full Links to Gbrowse: view cDNA, T-DNA Curated summary
- 7. SNP Discovery and Genetic Variation of Candidate Genes Relevant to Heat Tolerance and Agronomic Traits in Natural Populations of Sand Rice (Agriophyllum squarrosum) http://journal.frontiersin.org/article/10.3389/fpls.2017.00536/full Links to Gbrowse: view cDNA, T-DNA
- 8. What do similar genes do in other plants? Get sequences See GO annotations Find orthologs in different databases
- 9. What residues are conserved? Panther Tree View Multiple Sequence Alignment (MSA) Phylogenetic tree Protein alignment
- 10. Order stocks Click for more details What mutants/ variants exist ? What are the phenotypes?
- 11. What else is known about ELF3 in the literature?
- 12. http://www.arabidopsis.org/tools/go_term_enrichment.jsp Data Source: Nguyen, et al., Tomato Golden2-like transcription factors reveal molecular gradients that function during fruit development and ripening. ( https://doi.org/10.1105/tpc.113.118794)
- 13. We’d love to hear from you Visit us here at the AgBioData Booth # 215 and at Poster#100-017 get cool stickers Email us curator@arabidopsis.org
Editor's Notes
- The Arabidopsis Information Resource A curated reference resource for translational plant biology As presented in the Bioinformatics Resources Workshop ASPB 2017
- TAIR began in 1999 with the aim of providing a comprehensive, integrated portal into the Arabidopsis genome. Our primary focus has been on functional annotation of the Arabidopsis genome primarily by curating data from the published literature to make it more accessible to both humans and machines. We codify these results in the form of Gene Ontology Annotations , PO annotations. In addition we curate summaries and nomenclature as well as manual validation of literature association. A lot of this information is exported and used by other informatics resources such as Araport, Gramene and BAR.
- Experimental and non-experimental Gene Ontology Annotations. Arabidopsis is one of the most well annotated species and the most well annotated plant species.
- How are TAIR’s annotations useful to plant biologists
- Example of using TAIR to infer function of unknown gene in a non-model species.
- Navigating the information content in an example TAIR locus page. -Curated summary and gene nomenclature -Gene structure glyph links to G-Browse to visualize genomic context and structure -Curated annotations
- -Annotation detail page showing the expanded annotations -A basic annotation has a gene product, a Gene Ontology or Plant Ontology term, Evidence Code and a Reference. -Evidence codes can be used to assess the ‘strength of the assertion’. Manual, experimental based evidence codes include IDA (inferred from direct assay), IPI (inferred from physical interaction), IGI (inferred from genetic interaction), IEP (inferred from expression pattern, IMP (inferred from mutant phenotype). Other codes may be based on electronic inference methods such as ISS (inferred from sequence similarity)/
- New information on the locus page for Gene Families includes: -Links to orthology databases to search for orthologs of the locus of interest -Link out to the PANTHER database TreeViewer displaying the locus of interest in a phylogenetic context of its PANTHER gene family. -List of plant homologs from the PANTHER database
- Panther Phylogenetic Tree to display alignments
- Locus pages include alleles/polymorphisms and germplasms with curated phenotypes if they exist. -Find variants and assess the effects of variation in arabidopsis
- Locus page curated publication lists to find further information.
- TAIR contributes GO annotations to the GO consortium These GO annotations are updated quarterly, The PANTHER tool is recommended because it uses up to date datasets which is important for a genome like Arabidopsis where new information is being updated PANTHER tool also allows enrichment for 9 other plant species TAIR’s implementation accesses the PANTHER web service.