TAIR resources for plant biology research kate dreher curator TAIR/PMN.

TAIR resources for plant biology research

kate dreher

curator

TAIR/PMN

The Arabidopsis Information Resource: www.arabidopsis.org

Curation at TAIR Gene structure annotations Gene / protein functional annotations Partner with the PMN: Metabolic pathway curation

External resource integration at TAIR Data sets Biological materials Other databases

Introduction to TAIR

Curation at TAIR Gene structural curation

Use many different data types ESTs, cDNAs, peptides, RNASeq (new)

Determine gene coordinates and features Establish intron, exon, and UTR boundaries Add alternative splice variants Give “confidence” scores to show level of experimental support for each

exon and splice variant

Classify genes protein coding miRNA pseudogene

Keep updating! (even though the genome was sequenced in 2000!) TAIR9 – released June 2009 282 new loci and 739 new splice variants

Curation at TAIR

Gene/protein functional curation

Based on scientific literature and user submissions

GO functional annotations PO expression annotations Gene names and symbols Mutant phenotype descriptions Literature links

Continues . . . . . . it’s 2010, and we still don’t know what every Arabidopsis protein does

External resource integration at TAIR Data sets (viewable within TAIR)

Arabidopsis EST sequences Other plant EST sequences (selected dicots and monocots) Arabidopsis and Brassica cDNAs non-coding RNAs Alternative gene predictions Transcript expression data Peptide expression data Epigenetic features Ecotype-specific polymorphisms Promoter elements Post-translational modifications Interaction partners Orthologs Publications

Biological materials (provided by Arabidopsis Biological Resource Center-ABRC) Seed stocks DNA resources

External resource integration at TAIR Databases

Microarray expression (e.g. e-FP Browser) Co-expression analysis SNP viewer Ortholog sets Comparative genomics

External resource integration at TAIR Databases

Microarray expression (e.g. e-FP Browser) Co-expression analysis SNP viewer Ortholog sets Comparative genomics Biochemical pathways Proteomics Insertional mutant resources Subcellular localization Membrane proteins etc.

Pathway

EnzymeGene

ReactionCompound

Evidence Code

Accessing data and resources at TAIR Find your gene(s) of interest

Sequence similarity (BLAST or Patmatch) AGI locus code (e.g. At2g46990) or gene name (IAA20) Gene function Gene expression pattern Mutant phenotype Protein domain Protein biochemical properties Interaction with other proteins

Accessing data and resources at TAIR

Gather information about your gene(s) of interest Individual gene:

Locus page GBrowse NBrowse (interaction viewer) Synteny viewer

Multiple genes Bulk download tools ftp files

Putting TAIR to work for you . . .

You are studying drought tolerance in your species of interest

You identify ESTs that are up-regulated in the roots of drought-stressed plants

An EST that you name SECA1 appears to be present at particularly high levels

How can TAIR help?

What is the closest homolog to SECA1 in Arabidopsis? Blast SECA1 against the TAIR9 protein data set

BLASTX: NT query, AA db

What can you learn about the function of the SECA1 homolog?

Examine the locus page

What can you learn about the function of the SECA1 homolog?

Linksto other

databases

Publications

What can you learn about the function of the SECA1 homolog?

What phenotypes do xerico mutants have?

Germplasm/Seed stock

Available to order from

ABRC

Can I complement this phenotype using SECA1?

What can you learn about the function of the SECA1 homolog?

What will happen if I overexpress XERICO in my species?

What can you learn about the function of the SECA1 homolog?

What will happen if I overexpress XERICO in my species?

GBrowse

What is the sequence of the full-length SECA1 transcript and gene?

Is XERICO subjected to post-translational regulation?

What can you learn about the function of the SECA1 homolog?

Are there SECA1 / XERICO orthologs in other plants?

Are SECA1 / XERICO orthologs expressed in other plants?

What proteins does the SECA1 homolog interact with? Use NBrowse

Sometimes one gene isn’t enough

What if 50 other genes were up-regulated under drought stress, too?

Map them to AGI locus codes

Use bulk download tools to get their sequences GO terms gene descriptions etc.

What can we learn about all the up-regulated transcripts? Get the individual GO annotations for each gene

Get the description for each geneWhat can we learn about all the up-regulated transcripts?

Arabidopsis research can be successfully applied to “real plants”

Over-expression of the hardy gene from Arabidopsis can improve water use efficiency in rice (Karaba 2007)

Studies on a sodium transporter (HKT1) in Arabidopsis helped to identify a durum wheat homolog. It has been introgressed into bread wheat lines and appears to improve their yield on saline soils (Hwang 2006; Byrt 2007, et al)

We hope Arabidopsis and TAIR can help in your species of interest, too . . .

We are here to help: www.arabidopsis.org Please use the data we provide

Please use our tools

Please use TAIR to help further your research on important plants

Please contact us if we can be of any help! Make an appointment to meet with me during the conference Please come visit our exhibitor booth!

[email protected]

www.arabidopsis.org

AcknowledgementsTAIR

Current Curators:

- Tanya Berardini (lead curator – functional annotation)

- David Swarbreck (lead curator – structural annotation)

- Peifen Zhang (Director and lead curator- metabolism)

- Philippe Lamesch (curator)

- Donghui Li (curator)

- Debbie Alexander (curator)

- A. S. Karthikeyan (curator)

- Marga Garcia (curator)

- Leonore Reiser (curator)

Eva Huala (Director) Sue Rhee (Co-PI)

Tech Team Members:- Bob Muller (Manager)- Larry Ploetz (Sys. Administrator)- Raymond Chetty- Cynthia Lee- Shanker Singh- Chris Wilks

Recent Past Contributors:

- Anjo Chi (tech team)

- Vanessa Kirkup (tech team)

-Tom Meyer (tech team)

- Rajkumar Sasidharan (curator)