a guided tour of araport

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A Guided Tour of Araport

Agnes ChanJ Craig Venter

Institute

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Arabidopsis Information Portal(www.Araport.org)

ARAPORT.org

Where to find us?• Poster #286• Booth #504• araport@jcvi.org

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Which data resource do I need…

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A one-stop community platform(Built for and by the community)

•Data Integration•Data sharing by the community•Discovery & Analysis

Araport

Scientific Community

Data Sharing

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Araport Data Warehouse

• Gene Reports• Gene list analysis• Predefined queries• Custom data tables

Genome Browser• Over 100 tracks

• Araport11• RNA-seq datasets• 1001 genomes variants

• Upload your own tracks for local or public viewing

Community Data Modules• Data APIs• Compute Apps

ThaleMine JBrowse

Science AppsGenome Annotation• Latest gene models from

Maker, NCBI, UniProt• RNA-seq supported

isoforms• Updated functional names

Araport11

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https://www.Araport.org

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ThaleMine – Gene Report

FT

Provide a gene identifier

(e.g. FT or AT1G65480)

https://apps.araport.org/thalemine

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ThaleMine - Gene Report(FT gene, AT1G65480)

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ThaleMine - Gene Report(Expression, Interaction, Sequence)

FT gene, AT1G65480

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ThaleMine - Gene Report(Seed Stock, Genotype, Phenotype)

FT gene, AT1G65480

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ThaleMine – Gene List Analysis

• Create a list of genes– For example, from gene

expression profiling• Test for functional

enrichments of these categories– Gene Ontology– Pathways– Publications– Protein Domains– Chromosome Locations

araport.org@araport

ThaleMine – Gene List Analysis

• Create a list of genes– For example, from gene

expression profiling• Test for functional

enrichments of these categories– Gene Ontology– Pathways– Publications– Protein Domains– Chromosome Locations

araport.org@araport

ThaleMine – Saving and Sharing Gene Lists

• Create your gene lists for– Your own use– Sharing with collaborators– Publishing to the

community• Example gene lists– Loss-of-function mutant

gene lists from Lloyd and Meinke (2012)

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ThaleMine – Pre-defined Queries

• Browse and export data in ThaleMine

For example:– List seed stocks related to

“flowering”– List all interactors

(genetic and physical) for the FT gene

– Get gene expression values from different treatment conditions for a gene set

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ThaleMine – Build Your Own Query

Transparent data model for flexible query construction

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ThaleMine – A Simple Case Study

1. Flowering time (FT) gene,– Get a list of interacting partners (physical

and genetic)2. List of FT interacting genes,– Run functional enrichment analysis– Get expression values and export data

table for downstream analysis– Get gene and CDS sequences and export

in FASTA format

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(1) Use a Pre-defined Query to Get a List of Interacting Genes of FT

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(1) Use a Pre-defined Query to Get a List of Interacting Genes of FT

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(2a) Create Gene List & Run Gene List Analysis

A Gene List Analysis is automatically run each time a gene list is called.

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(3b) Get Expression Values and Export Data

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(3b) Get Expression Values and Export Data

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ThaleMine – Integrated Public Data Sources

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JBrowse – Over 100 data tracks(Araport11, RNA-seq, T-DNA, …)

https://apps.araport.org/jbrowse

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JBrowse – Community Data Tracks(1001 Genomes, Phytozome, EPIC-CoGe, ...)

1001Phytozome

EPIC-CoGe

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JBrowse – Build Your Own Tracks• Data track for your own use

– Upload your files directly to Araport JBrowse– FAQ: https://www.araport.org/help/faq#t349n244

• Data track for specific sharing with collaborators– Upload your files to the iPlant/CyVerse Data Store (GFF,

BAM, VCF); Share URL links with collaborators– FAQ: https://www.araport.org/help/faq#t349n66

• Data track for broad sharing with community– Demo example: Predicted chromatin states from Sequeira-

Mendes et al. (2014)– Publishing mechanism planned in early 2016

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JBrowse – Build Your Own Tracks(Local Use or Sharing with Collaborators)

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JBrowse – Build Your Own Tracks(Public Data Sharing Mechanism Coming Soon)

Demo case: Predicted chromatin States Sequeira-Mendes et al. (2014) Plant Cell

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Araport11 Genome Annotation

Araport11Protein Coding

Genes

UniProt

Update

NCBI Novel Model

s

Maker Novel Model

s

NCBI SRA

RNA-seq

PASA, Trinity, BLAST,…

https://www.araport.org/data/araport11

TAIR10Annotati

on

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Araport11 Pre-release 3 (Dec 2015)

• Available via ThaleMine, JBrowse, FTP, APIs

Categories TAIR10 Araport11Gene LociProtein coding loci 27,416 27,667Novel loci in Araport11 719Gene loci with splice isoform 5,665 10,698TranscriptsTranscript isoforms 35,385 48,389Transcripts altered in Araport11CDS altered 1,191UTR altered 24,185

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A one-stop community platform(Built for and by the community)

•Data Integration•Data sharing by the community•Discovery & Analysis

Araport

Scientific Community

ThaleMine gene lists

JBrowse data

tracks

Community Data Modules

(Upcoming talks)

araport.org@araport

AcknowledgementsJ Craig Venter Institute• Chris Town• Jason Miller• Agnes Chan• Vivek Krishnakumar• Chia-Yi Cheng• Erik Ferlanti• Irina Belyaeva

University of Cambridge• Gos Micklem• Sergio Contrino

Former members• Ben Rosen• Svetlana Karamycheva• Eleanor Pence• Maria Kim• Seth Schobel

Texas Advanced Computing Center• Matt Vaughn• Steve Mock• Rion Dooley• Matt Hanlon• Joe Stubbs• Walter Moreira

TAIR• Eva Huala• Bob Muller