What's New at Araport - ICAR 2017

Presented in the "New and Updated Bioinformatics Datasets, Tools and Resources" at the 28th International Conference on Arabidopsis Research (ICAR 2017) held in St. Louis, MO.

Presented on Thursday, June 22nd, 2017 by Vivek Krishnakumar

Transcript

1. araport.org
   @araport
   What’s New
   at Araport?
   Vivek Krishnakumar
   J. Craig Venter Institute
   @vivekkrish
   

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2. araport.org
   @araport
   Arabidopsis Information Portal
   www.Araport.org
   araport@jcvi.org
   co-PI Matt Vaughn co-PI Gos Micklem
   PI Chris Town
   co-PI Agnes Chan
   

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3. araport.org
   @araport
   Data Integration
   Discovery and Analysis
   Data sharing and reuse
   Araport
   Scientific
   Community
   A One-Stop Data Platform
   Built for and by the Community
   

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4. araport.org
   @araport
   Genome Browser
   • Over 100 tracks
   • Araport11
   • RNA-seq datasets
   • 1001 genomes variants
   Community Modules
   • Data APIs
   • Compute Apps
   Araport – Data Sharing and Reuse
   Data Warehouse
   • Gene Reports
   • Gene list analysis
   • Predefined queries
   • Custom data tables
   ThaleMine JBrowse
   Web Services
   Genome Annotation
   • Latest gene models from NCBI,
   UniProt, MAKER
   • RNA-seq supported isoforms
   • Update protein product names
   Araport11
   

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5. araport.org
   @araport
   https://www.Araport.org
   

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6. araport.org
   @araport
   Community
   Orthologs
   (PhytoMine)
   Co-expression
   (ATTED)
   Real-time
   Data Centers
   Community
   Protein Interactions
   (InAct, BioGrid)
   Gene expression
   (Araport, BAR)
   Publications
   (NCBI, UniProt)
   Pathways
   (KEGG)
   Core
   ThaleMine
   Gene List
   Analysis
   Gene
   Report
   Query,
   Data Tables
   Web
   Services
   ThaleMine - Data Warehouse
   Warehouse
   Araport
   Data Sources
   Krishnakumar et al 2016, Plant Cell Physiol.
   Col-0 genome &
   annotation
   (Araport11, TAIR)
   

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7. araport.org
   @araport
   ThaleMine –
   Gene Report
   FT gene, AT1G65480
   

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8. araport.org
   @araport
   ThaleMine – Gene List Analysis
   • Create a list of genes
   – For example, from gene
   expression profiling
   • Test for functional
   enrichments of:
   – Gene Ontology
   – Pathways
   – Publications
   – Protein Domains
   – Chromosome Locations
   Test for functional enrichments of gene lists
   

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9. araport.org
   @araport
   ThaleMine – Build Your Own Query
   Transparent data model for flexible query construction
   

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10. araport.org
    @araport
    Common Data Model Enables Crosstalk
    Between Resources
    ThaleMine
    PhytoMine
    SoyMine
    Peanut
    Mine
    Bean
    Mine
    Medic
    Mine
    Cowpea
    Mine
    Legume Federation
    JGI
    Araport
    Human
    Model Organisms
    Yeast
    …and more
    …and more
    • Orthology
    • Synteny
    

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11. araport.org
    @araport
    ThaleMine – Recently Added
    Heatmap for 113 RNA-Seq Studies
    Gene Report
    Gene List Analysis
    Ortholog links to other InterMines
    Gene Report (e.g. dicer-like 1/AT1G01040)
    Medicago
    JGI PhytoMine
    Human
    RNA-seq study
    RNA-seq study
    Gene
    Genes
    

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12. araport.org
    @araport
    https://www.Araport.org
    

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13. araport.org
    @araport
    JBrowse – Over 100 Data Tracks
    RNA-seq
    T-DNA
    Phytozome
    Vista plot
    Araport11
    

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14. araport.org
    @araport
    JBrowse - Self-Service Data Sharing
    Araport
    JBrowse
    Your genomic
    feature files
    Variants (VCF)
    Alignments (BAM)
    Genes & Features
    (GFF3, BED)
    Discovery Environment
    (DE) Workflow
    Data Store
    Output
    User upload
    JBrowse
    plugin
    App
    (Data + Metadata)
    

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15. araport.org
    @araport
    JBrowse – Self-Service Prototype
    Seeding miRNA-Seq
    Seedling RNA-Seq reads
    Pollen RNA-Seq junctions
    Community Data Tracks
    Araport11 gene models
    Your genomic feature data will
    be displayed in the JBrowse
    menu and data tracks
    

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16. araport.org
    @araport
    Protein-coding
    Genes
    uORF
    Non-coding
    Genes
    Genomic
    Features
    Small
    RNAs
    Novel Transcribed
    Regions
    snoRNA
    tRNA, rRNA
    NAT
    miRNA
    lincRNA
    snRNA
    Gene Loci
    Transcript
    Variants
    35,386 -> 48,359
    (113 RNA-seq Datasets)
    177 -> 325 (miRBase)
    223 -> 1,115 (Publication)
    36 -> 2,444 (Publication)
    71 -> 287 (Publication)
    13 -> 82 (Publication)
    No change
    TAIR10 counts -> Araport11
    counts (Evidence type)
    na -> 508 (RNA-seq)
    58 -> 84 (Publication)
    na -> 35,846 (Prediction)
    27,416 -> 27,655
    (NCBI, Maker, UniProt;
    Retired loci: 452 short
    coding sequences)
    Data available via NCBI,
    ThaleMine, JBrowse, FTP,
    and Araport web services
    Cheng, Krishnakumar et al 2016, Plant Journal
    Araport11 Col-0 reannotation
    

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17. araport.org
    @araport
    Araport Web Services
    Examples of APIs developed by the Araport team, and collaborators including
    BAR, CoGe, ATTED-II, PMR, HRGRN, SUBA, and iHub.
    

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18. araport.org
    @araport
    Araport – Data Sharing and Reuse
    ePlant (BAR)
    ThaleMine
    Co-expression
    (ATTED)
    Gene Networks
    (HRGRN)
    Subcellular
    Localization (SUBA)
    Metabolomics
    (PMR)
    Ionomics
    (iHub)
    Community
    Community
    Apps
    Community
    resources
    Orthologs
    (PLAZA)
    1001
    Genomes
    Synteny
    (CoGe)
    Context Viewer
    (NCGR)
    Community
    Araport Web Services
    Comparative
    Genomics
    Stocks (ABRC,
    NASC, RIKEN)
    Locus
    Detail (TAIR)
    Text Mining
    (DIVE)
    

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19. araport.org
    @araport
    Araport – Data Sharing and Reuse
    ePlant (BAR)
    ThaleMine
    Co-expression
    (ATTED)
    Gene Networks
    (HRGRN)
    Subcellular
    Localization (SUBA)
    Metabolomics
    (PMR)
    Ionomics
    (iHub)
    Community
    Community
    Apps
    Community
    resources
    Orthologs
    (PLAZA)
    1001
    Genomes
    Stocks (ABRC,
    NASC, RIKEN)
    Locus
    Detail (TAIR)
    Synteny
    (CoGe)
    Context Viewer
    (NCGR)
    Community
    Araport Web Services
    Comparative
    Genomics
    Text Mining
    (DIVE)
    

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20. araport.org
    @araport
    Acknowledgements
    J Craig Venter Institute
    • Chris Town
    • Agnes Chan
    • Vivek Krishnakumar
    University of Cambridge
    • Gos Micklem
    • Sergio Contrino
    Former members
    • Jason Miller
    • Ben Rosen
    • Chia-Yi Cheng
    • Svetlana Karamycheva
    • Irina Belyaeva
    • Maria Kim
    • Seth Schobel
    • Eleanor Pence
    • Matthew Hanlon
    • Walter Moreira
    Texas Advanced Computing Center
    • Matt Vaughn
    • Steve Mock
    • Rion Dooley
    • Joe Stubbs
    • Josue Coronel
    • Erik Ferlanti
    TAIR/Phoenix
    • Eva Huala
    • Bob Muller
    

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21. araport.org
    @araport
    Thank you!
    araport@jcvi.org
    Poster #310
    Thu Jun 22, 8:00pm
    Grand Ballroom ABCD
    Arabidopsis Information Portal
    www.Araport.org
    

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