4. araport.org@araport
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
5. araport.org@araport
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 Apps
Genome Annotation
• Latest gene models from
Maker, NCBI, UniProt
• RNA-seq supported isoforms
• Updated functional names
Araport11
11. 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
12. 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
13. 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)
14. araport.org@araport
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
16. araport.org@araport
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
25. araport.org@araport
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
29. araport.org@araport
Araport11 Pre-release 3 (Dec 2015)
• Available via ThaleMine, JBrowse, FTP, APIs
Categories TAIR10 Araport11
Gene Loci
Protein coding loci 27,416 27,667
Novel loci in Araport11 719
Gene loci with splice isoform 5,665 10,698
Transcripts
Transcript isoforms 35,385 48,389
Transcripts altered in Araport11
CDS altered 1,191
UTR altered 24,185
30. araport.org@araport
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)
31. araport.org@araport
Acknowledgements
J 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
Editor's Notes
I am going to introduce the different components of Araport, and how you can use it for your research.
Funding agencies
Participating institutes
Let’s start with a common obstacle in biological research.
There are now a large number of data resources.
Which resource do I need?
We would often need to visit and explore many sites to collect the data needed.
The goal of Araport is to develop a community platform:
-to integrate the many heterogeneous data types into a single resource
Data integration, sharing and discovery
Araport is a one-stop-shop built for (and by) the community.
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
Example: FT gene, Data one-click away
-Browse and export gene data
Publication table
GO table
Coexpression table
Homology table
Interaction table
Pathway table
-Basic tools:
Export sequence (gene, UTR, flanking) in fasta format
Export data table
The goal of Araport is to develop a community platform:
-to integrate the many heterogeneous data types into a single resource
Data integration, sharing and discovery
Araport is a one-stop-shop built for (and by) the community.