Upgrade to Pro — share decks privately, control downloads, hide ads and more …

What's New at Araport - ICAR 2017

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

Vivek Krishnakumar

June 22, 2017
Tweet

More Decks by Vivek Krishnakumar

Other Decks in Science

Transcript

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

    View Slide

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

    View Slide

  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

    View Slide

  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

    View Slide

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

    View Slide

  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)

    View Slide

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

    View Slide

  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

    View Slide

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

    View Slide

  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

    View Slide

  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

    View Slide

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

    View Slide

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

    View Slide

  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)

    View Slide

  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

    View Slide

  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

    View Slide

  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.

    View Slide

  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)

    View Slide

  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)

    View Slide

  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

    View Slide

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

    View Slide