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
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
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
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
5. araport.org @araport https://www.Araport.org
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)
7. araport.org @araport ThaleMine – Gene Report FT gene, AT1G65480
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
9. araport.org @araport ThaleMine – Build Your Own Query Transparent data model for flexible query construction
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
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
12. araport.org @araport https://www.Araport.org
13. araport.org @araport JBrowse – Over 100 Data Tracks RNA-seq T-DNA Phytozome Vista plot Araport11
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)
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
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
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.
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)
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)
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
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