The document summarizes updates and new features in the latest release (Araport11) of the Arabidopsis Information Portal (Araport). Key points include: 1) Araport assumed responsibility for the Arabidopsis thaliana Col-0 genome sequence and annotation. 2) The Araport11 release incorporates 113 RNA-seq datasets, contributions from NCBI, UniProt, and Arabidopsis researchers. Structural and functional annotation were performed. 3) Araport provides a "one-stop shop" for Arabidopsis data including updated gene models, protein coding genes, transcripts, community curation tools, and over 70 tracks of data in JBrowse.

1. Agnes Chan1, Vivek Krishnakumar1, Chia-Yi Cheng1, Maria Kim1, Erik Ferlanti1, Irina Belyaeva1, Seth Schobel1, Sergio
Contrino3, Matthew R. Hanlon2, Walter Moreira2, Steve Mock2, Joe Stubbs2, Jason R. Miller1, Matthew W. Vaughn2, Gos
Micklem3, Christopher D. Town1
1J. Craig Venter Institute, Rockville, MD, USA; 2Texas Advanced Computing Center, Austin, TX, USA;3Cambridge University, Cambridge, UK
Col-0 Genome Reannotation, Araport11 Pre-release
Araport was funded by NSF and BBSRC to develop the Arabidopsis Information
Portal aimed at providing a one-stop-shop for a wide range of data sets. As part
of its mandate, Araport assumed the responsibility for the Col-0 genome
sequence and annotation.
In the Araport11 release, we made use of 113 RNA-seq data sets along with
annotation contributions from NCBI, UniProt, and labs conducting Arabidopsis
thaliana research. Structural and functional annotation have been performed.
Consolidation and annotation of non-coding RNAs is currently in progress.
Araport - A“One-Stop” data shop for the 21st century
www.ARAPORT.org
Araport11 Protein
Coding Genes
UniProt
Update
NCBI
Novel
Updated
Transcripts
Novel
Transcripts
Transcripts
No Change
Maker
Novel
NCBI SRA
RNA-seq
(113 datasets)
PASA
Update
Trinity
Assembly
Web Apollo Community Annotation
Web Apollo is available for the Arabidopsis community to curate and submit
gene edits. Web Apollo uses a JBrowse interface and gene edits are instantly
viewable by others, allowing the community to see and share annotation in real-
time - just like Google Doc.
What will happen to your curation? Community curation will be regularly
reviewed by curators at Araport, published as a community curation track at the
Araport JBrowse, with attributions to the contributors.
AraportUsers Data Sources
Biologists/
Bioinformaticans
• Users who use detailed gene
reports, protein reports,
germplasm reports, or integrated
data.
• Users who perform analyses such
as GO term or pathway
enrichment for gene lists.
• Users who access data via web
services or bulk downloads.
Software Developers
• Users who use Araport tools to
expose their own data via
interoperable web services.
• Users who use Araport tools to
create science apps for analysis,
visualization, and data
integration.
1001 Genomes
Variants
(Ensembl)
Epigenetics
(EPIC-CoGe)
TDNA-seq (Ecker)
and over 70 tracks
Co-expression
(ATTED)
ePictographs
(BAR)
Array Expression,
Interactions (BAR)
Win an iPad
Developers’
Workshop
Fall 2015
ThaleMine
Chado
Gene
Report
Gene List
Analysis
Query,
Web Services
JBrowse
Custom
Analysis
Science
Apps
Araport11
• Updated models
• RNA-seq by tissue
Warehousing
Publications,
GeneRIF
(NCBI, UniProt)
TAIR10
Real-time
Real-time
Categories TAIR10 Araport11
Gene Loci
Protein coding loci 27,416 28,565
Novel loci in Araport11 1,162
Gene loci with splice isoform 5,665 10,946
Transcripts
Transcript isoforms 35,385 50,203
Transcripts altered in Araport11
CDS altered 933
UTR altered 25,079
Community
Data/Tools
JBrowse provides over 70 tracks of data
including RNA-seq expression, 1001
genomes variants, TDNA-seq locations, and
epigenomics data are available.
A new variant data filter feature helps
users to select for variants based on
functional consequences. Click on the 1001
track menu (purple box below) to access the
data filter function.
ThaleMine Data Warehouse
ThaleMine Gene Report presents integrated data from a variety sources, including GO
annotation, array expression, co-expression, interactions, pathways, publications and
homologs. Germplasm, genotype, phenotype data are coming soon.
ThaleMine List Analysis tests for functional enrichments for GO terms, pathways,
domains, publications, and chromosome distribution given a gene list of interest.
Germplasm
• Genotype
• Phenotype
Warehousing
Interactions Pathways List Analysis
Data Summary Data Model
Web Apollo
Variant Data Filter
Pathways
(KEGG)
~16,000 ~1,200
~26,000
Google Play
Android App
1. Araport: the Arabidopsis Information
Portal. Nucleic Acids Research (2015),
43: D1003-9. PMID: 25414324
2. The Arabidopsis Information Portal: An
Application Platform for Data Discovery.
Proceedings of the 9th Gateway
Computing Environments Workshop
(2014) doi: 10.1109/GCE.2014.10
JBrowse References
Bulletin BoardGene Edit
Real-time