A guided tour of Araport
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A guided tour of Araport
- 1. araport.org@araport A Guided Tour of Araport Agnes Chan J Craig Venter Institute
- 2. araport.org@araport Arabidopsis Information Portal (www.Araport.org) ARAPORT.org Where to find us? • Poster #286 • Booth #504 • araport@jcvi.org
- 3. araport.org@araport Which data resource do I need…
- 4. araport.org@araport A one-stop community platform (Built for and by the community) •Data Integration •Data sharing by the community •Discovery & Analysis Araport Scientific Community Data Sharing
- 5. araport.org@araport Araport Data Warehouse • Gene Reports • Gene list analysis • Predefined queries • Custom data tables Genome Browser • Over 100 tracks • Araport11 • RNA-seq datasets • 1001 genomes variants • Upload your own tracks for local or public viewing Community Data Modules • Data APIs • Compute Apps ThaleMine JBrowse Science Apps Genome Annotation • Latest gene models from Maker, NCBI, UniProt • RNA-seq supported isoforms • Updated functional names Araport11
- 7. araport.org@araport ThaleMine – Gene Report FT Provide a gene identifier (e.g. FT or AT1G65480) https://apps.araport.org/thalemine
- 8. araport.org@araport ThaleMine - Gene Report (FT gene, AT1G65480)
- 9. araport.org@araport ThaleMine - Gene Report (Expression, Interaction, Sequence) FT gene, AT1G65480
- 10. araport.org@araport ThaleMine - Gene Report (Seed Stock, Genotype, Phenotype) FT gene, AT1G65480
- 11. araport.org@araport ThaleMine – Gene List Analysis • Create a list of genes – For example, from gene expression profiling • Test for functional enrichments of these categories – Gene Ontology – Pathways – Publications – Protein Domains – Chromosome Locations
- 12. araport.org@araport ThaleMine – Gene List Analysis • Create a list of genes – For example, from gene expression profiling • Test for functional enrichments of these categories – Gene Ontology – Pathways – Publications – Protein Domains – Chromosome Locations
- 13. araport.org@araport ThaleMine – Saving and Sharing Gene Lists • Create your gene lists for – Your own use – Sharing with collaborators – Publishing to the community • Example gene lists – Loss-of-function mutant gene lists from Lloyd and Meinke (2012)
- 14. araport.org@araport ThaleMine – Pre-defined Queries • Browse and export data in ThaleMine For example: – List seed stocks related to “flowering” – List all interactors (genetic and physical) for the FT gene – Get gene expression values from different treatment conditions for a gene set
- 15. araport.org@araport ThaleMine – Build Your Own Query Transparent data model for flexible query construction
- 16. araport.org@araport ThaleMine – A Simple Case Study 1. Flowering time (FT) gene, – Get a list of interacting partners (physical and genetic) 2. List of FT interacting genes, – Run functional enrichment analysis – Get expression values and export data table for downstream analysis – Get gene and CDS sequences and export in FASTA format
- 17. araport.org@araport (1) Use a Pre-defined Query to Get a List of Interacting Genes of FT
- 18. araport.org@araport (1) Use a Pre-defined Query to Get a List of Interacting Genes of FT
- 19. araport.org@araport (2a) Create Gene List & Run Gene List Analysis A Gene List Analysis is automatically run each time a gene list is called.
- 20. araport.org@araport (3b) Get Expression Values and Export Data
- 21. araport.org@araport (3b) Get Expression Values and Export Data
- 22. araport.org@araport ThaleMine – Integrated Public Data Sources
- 23. araport.org@araport JBrowse – Over 100 data tracks (Araport11, RNA-seq, T-DNA, …) https://apps.araport.org/jbrowse
- 24. araport.org@araport JBrowse – Community Data Tracks (1001 Genomes, Phytozome, EPIC-CoGe, ...) 1001 Phytozome EPIC-CoGe
- 25. araport.org@araport JBrowse – Build Your Own Tracks • Data track for your own use – Upload your files directly to Araport JBrowse – FAQ: https://www.araport.org/help/faq#t349n244 • Data track for specific sharing with collaborators – Upload your files to the iPlant/CyVerse Data Store (GFF, BAM, VCF); Share URL links with collaborators – FAQ: https://www.araport.org/help/faq#t349n66 • Data track for broad sharing with community – Demo example: Predicted chromatin states from Sequeira- Mendes et al. (2014) – Publishing mechanism planned in early 2016
- 26. araport.org@araport JBrowse – Build Your Own Tracks (Local Use or Sharing with Collaborators)
- 27. araport.org@araport JBrowse – Build Your Own Tracks (Public Data Sharing Mechanism Coming Soon) Demo case: Predicted chromatin States Sequeira- Mendes et al. (2014) Plant Cell
- 28. araport.org@araport Araport11 Genome Annotation Araport11 Protein Coding Genes UniProt Update NCBI Novel Models Maker Novel Models NCBI SRA RNA-seq PASA, Trinity, BLAST,… https://www.araport.org/data/araport11 TAIR10 Annotatio n
- 29. araport.org@araport Araport11 Pre-release 3 (Dec 2015) • Available via ThaleMine, JBrowse, FTP, APIs Categories TAIR10 Araport11 Gene Loci Protein coding loci 27,416 27,667 Novel loci in Araport11 719 Gene loci with splice isoform 5,665 10,698 Transcripts Transcript isoforms 35,385 48,389 Transcripts altered in Araport11 CDS altered 1,191 UTR altered 24,185
- 30. araport.org@araport A one-stop community platform (Built for and by the community) •Data Integration •Data sharing by the community •Discovery & Analysis Araport Scientific Community ThaleMine gene lists JBrowse data tracks Community Data Modules (Upcoming talks)
- 31. araport.org@araport Acknowledgements J Craig Venter Institute • Chris Town • Jason Miller • Agnes Chan • Vivek Krishnakumar • Chia-Yi Cheng • Erik Ferlanti • Irina Belyaeva University of Cambridge • Gos Micklem • Sergio Contrino Former members • Ben Rosen • Svetlana Karamycheva • Eleanor Pence • Maria Kim • Seth Schobel Texas Advanced Computing Center • Matt Vaughn • Steve Mock • Rion Dooley • Matt Hanlon • Joe Stubbs • Walter Moreira TAIR • Eva Huala • Bob Muller
Editor's Notes
- I am going to introduce the different components of Araport, and how you can use it for your research.
- Funding agencies Participating institutes
- Let’s start with a common obstacle in biological research. There are now a large number of data resources. Which resource do I need? We would often need to visit and explore many sites to collect the data needed.
- The goal of Araport is to develop a community platform: -to integrate the many heterogeneous data types into a single resource Data integration, sharing and discovery Araport is a one-stop-shop built for (and by) the community.
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- Example: FT gene, Data one-click away -Browse and export gene data Publication table GO table Coexpression table Homology table Interaction table Pathway table -Basic tools: Export sequence (gene, UTR, flanking) in fasta format Export data table
- The goal of Araport is to develop a community platform: -to integrate the many heterogeneous data types into a single resource Data integration, sharing and discovery Araport is a one-stop-shop built for (and by) the community.