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New data and tools at TAIR
(The Arabidopsis Information Resource)
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Overview of TAIR
Genome release
Published papers
Gene function
Journal collaborations
Direct submission
RNA-seq Proteomic Corrections
Other data:MarkersEcotypes
Gene symbolsNew genomes
New tools
ResearchersDirectly (TAIR pages)AND via other databases
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TAIR10 Genome Release
Genome release
RNA-seq Proteomic Corrections • No assembly updates
• Will incorporate: – 200M Ecker and Mockler
RNA-seq reads– Additional proteomics data– Individual gene structure
corrections sent to us
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Mapping and Assembly1. Mapping• RNA-seq sequences (Tophat (C. Trapnell),
Supersplat (T.C. Mockler))• Peptides (6-frame translation, spliced exon graph)
2. Assembly approaches• Augustus (M. Stanke)o Uses spliced RNA seq reads, peptideso Aim: Identify additional splice-variants, update existing
genes• TAU (T.C. Mockler)o Uses spliced RNA seq readso Aim: Identify additional splice-variants• Cufflinks (C. Trapnell)o Uses spliced and unspliced RNA seq datao Aim: Identify novel genes
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Preliminary Results
Augustus/TAU/Cufflinks predicted models are classified into categories:
Novel genes 21
Updated genes 812
Splice-variants 2134
B-list 1586
Rejects 2318
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TAIR10 Genome Release
Genome release
RNA-seq Proteomic Corrections • No assembly updates
• Will incorporate: – 200M Ecker and Mockler
RNA-seq reads– Additional proteomics data– Individual gene structure
corrections sent to us
• Release expected in August 2010
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Experimentally Verified Gene Function
• From research articles read by TAIR curators
• From TAIR’s collaboration with journals
• From direct submissions by researchers to TAIR
Published papers
Gene function
Journal collaborations
Direct submission
Where does it come from???
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• How?– Papers are prioritized
according to novelty of gene function results
– Highest priority papers are read and gene function is extracted
• Why?– A lot of high quality
experimental gene function information is only available in the form of articles
• How many?– About 1/3 of all new articles
containing gene function data are curated at TAIR each year
Published papers
Gene function
Literature Curation
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• How?– Author instructions, Excel
sheet or online form
• Why?– To capture a larger fraction of
gene function data– Because publication is the
right time to get the data into TAIR
• What journals?
Gene function
Journal collaborations
Journal Collaboration
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Journal Collaboration
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• How?– Author instructions, Excel
sheet or online form
• Why?– To capture a larger fraction of
gene function data– Because publication is the
right time to get the data into TAIR
• What journals?
Gene function
Journal collaborations
2010:Journal of Integrative Plant BiologyJournal of Experimental BotanyPlant ScienceEnvironmental BotanyPlant Physiology and BiochemistryPlant, Cell and Environment
Plant Physiology (2008)
The Plant Journal (2009)
Journal Collaboration
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Direct Submission of Gene Function
• How?– Excel sheet or online form
• Why?– To capture more data with a
small curation team– Because researchers are the
experts on the genes they study
Gene function
Direct submission
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New online submission form
17986450
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Why Gene Ontology?
• Standardization allows comparison across experiments and species
• Hierarchical structure allows high level categorization
• Well structured ontology framework facilitates computational analysis
• Attached to data source (peer reviewed published research)
• Experimental evidence can be distinguished from predictions
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Example Gene Ontology annotations
Gene GO term Evidence Reference
Phot1 Phototropism Mutant phenotype Huala et al 1997
Phot1 Cytoplasm Direct assay Sakamoto et al 2002
Phot1 Serine / threonine kinase activity
Direct assay Christie et al 1998
Biological process
Cellular component
Molecular function
3 GO flavors
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New online submission form
Autocomplete (just start typing to get a list of matching terms)
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New online submission form
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New online submission form
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What is the result of TAIR’s effort to capture gene function?
• How many genes have experimental gene function in TAIR?
Published papers
Gene function
Journal collaborations
Direct submission
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Num
ber
of g
enes
9342 genes (May 31 2010)
Genes in TAIR with experimental evidence for biological process, molecular function or cellular component
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Arabidopsis Gene Function in TAIR
Year
Ge
nes
Protein coding genes
Predicted function
Experimental function
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Ara-bidopsis
yeast worm fly ze-brafish
mouse rat0
1000
2000
3000
4000
5000
6000
7000
8000
Experimental GO Annotations
Biological Process
Cellular Component
Molecular Function
Organism
Nu
mb
er
of
gen
e p
rod
ucts
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Overview of TAIR
Genome release
Published papers
Gene function
Journal collaborations
Direct submission
RNA-seq Proteomic Corrections
Other data:MarkersEcotypes
Gene symbolsNew genomes
New tools
ResearchersDirectly (TAIR pages)AND via other databases
![Page 26: New data and tools at TAIR (The Arabidopsis Information Resource)](https://reader031.vdocuments.site/reader031/viewer/2022033005/56649e685503460f94b6532b/html5/thumbnails/26.jpg)
GBrowse_syn
Tool by Sheldon McKay, CSHLAlignment data from Pedro Pattyn, Van de Peer lab, U. of Ghent
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GBrowse_syn
A. lyrata
A. thaliana
poplar
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NBrowse
Tool by H.-L. Kao, F. Piano, M. Schuman, M. Gibson, Kris Gunsalus, NYUInteraction datasets curated by TAIR, BioGRID and IntAct
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NBrowse
Tool by H.-L. Kao, F. Piano, M. Schuman, M. Gibson, Kris Gunsalus, NYUInteraction datasets curated by TAIR, BioGRID and IntAct
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NBrowse
Tool by H.-L. Kao, F. Piano, M. Schuman, M. Gibson, Kris Gunsalus, NYUInteraction datasets curated by TAIR, BioGRID and IntAct
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Genes have been loaded
Working on adding some gene function information and improving searching
Arabidopsis lyrata
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Overview of TAIR
Genome release
Published papers
Gene function
Journal collaborations
Direct submission
RNA-seq Proteomic Corrections
Other data:MarkersEcotypes
Gene symbolsNew genomes
New tools
ResearchersDirectly (TAIR pages)AND via other databases
![Page 35: New data and tools at TAIR (The Arabidopsis Information Resource)](https://reader031.vdocuments.site/reader031/viewer/2022033005/56649e685503460f94b6532b/html5/thumbnails/35.jpg)
Central registry for Gene Symbols
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Central registry for Gene Symbols
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Central registry for Gene Symbols
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Central registry for Gene Symbols
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Helpdesk
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Helpdesk
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Helpdesk
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RSS news feed
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RSS news feed
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TAIR Facebook Page
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TAIR Twitter Feed
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Tanya Berardini Donghui Li
Gene Function/GO:
Bob Muller Larry Ploetz Chris Wilks (50%)
?
David Swarbreck Philippe Lamesch Rajkumar Sasidharan
Genome Annotation:
TAIR Staff
Tech Team:
Cynthia LeeShanker Singh
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TAIR Sponsors:
Funding Agencies:
Host Institution: Partner: