A guided tour of Araport
Transcript of 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• [email protected]
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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
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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
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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