The Arabidopsis Information Resource (TAIR) is a curated reference database for plant biology that provides manual annotation of genes including Gene Ontology terms, summaries, and links to relevant publications, as well as information on alleles, phenotypes, and orthologs to aid in comparative functional analysis of genes across species. TAIR annotations serve as a "gold standard" and can be used to infer functions of unknown genes, classify gene lists, and transfer annotations to other plants based on sequence similarity. The database helps researchers investigate candidate genes related to traits like heat tolerance in non-model plants like sand rice by providing functional information on Arabidopsis orthologs.
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
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
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.
