icar 2015 poster - araport
Post on 17-Aug-2015
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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.
Araport Users 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 Board Gene Edit
Real-time
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