1. PAG 2015 Justin Preece Jaiswal Lab, Oregon State University 13 January 2015

2. PAG 2015 Plant Reactome Overview Pathway Curation Orthology Projections New software platform

3. PAG 2015 Plant Reactome: Overview What is Plant Reactome?  Curated metabolic & regulatory pathways in rice and Arabidopsis  Orthology projections to 33 other plant species, including maize and several other Oryza species  Gene expression overlays, visual species comparisons, other analysis tools (ongoing development)

4. PAG 2015 Reactome data model Depicts biological processes as a set of connected reactions and events It can represent many events and states in biological processes In addition to classical biochemical reactions, changes in state, such as binding, activation, translocation and degradation can be represented Reactions are connected to form pathways Plant Reactome: Overview

5. PAG 2015 Plant Reactome: Overview

6. PAG 2015 Plant Reactome: Overview

7. PAG 2015 Plant Reactome: Overview  Pathway Browser  Quick Search  Release News  Downloads  Projection Stats

8. PAG 2015 Plant Reactome: Overview Pathway browser

9. PAG 2015 Plant Reactome: Overview Search capabilities

10. PAG 2015 Additional search features and downloads Plant Reactome: Overview

11. PAG 2015 Orthology Projections

12. PAG 2015 Orthology Projections  Projections from O.sativa to 33 species using Reactome “orthology inference” software  Data sources :: Methods  Ensembl Gramene – 27 species (monocots and dicots) :: Compara  Published leaf tissue transcriptomes – 6 add’l Oryza taxa :: InParanoid clustering  Prepared orthology mapping files using custom Python script “Incomparanoid”

13. PAG 2015 Orthology projections Homologs of taxa listed in green are generated via Inparanoid clustering. * Data from sequenced transcriptome Relative projection “saturation”: Blue is highest, red lowest, with yellow marking the intermediate. ^Projections currently exclude cell-cycle pathways SpeciesPathwaysReactionsGene Products Oryza sativa japonica Nipponbare (curated reference) 238^1056935 Arabidopsis thaliana 184493832 Brassica rapa 1834921283 Glycine max (soybean) 1814831494 Medicago truncatula 171410643 Populus trichocarpa 1824841045 Prunus persica (peach) 184494713 Solanum lycopersicum (tomato) 183491873 Solanum tuberosum (potato) 180469844 Triticum aestivum (wheat ABD-genome hexaploid) 1855121841 Triticum urartu (wheat A-genome) 180470672 Aegilops tauschii (wheat D-genome) 177461731 Hordeum vulgare (barley) 177448627 Setaria italica (foxtail millet) 185511833 Brachypodium distachyon 181507745 Oryza rufipogon 186514779 Oryza nivara 185521773 Oryza sativa Indica (93-11) 189534836 Oryza sativa aus Kasalath 123205165 Oryza glumaepatula 187520770 Oryza barthii 186517769 Oryza glaberrima 188513769 Oryza longistaminata * 179475622 Oryza meridionalis 180475682 Oryza punctata 184508765 Oryza minuta * 172447556 Oryza officinalis * 178434474 Oryza australiensis * 174444734 Oryza granulata * 175450789 Oryza brachyantha 186509741 Leersia perrieri 186506731 Sorghum bicolor 186514802 Zea mays 184506950 Musa acuminata (banana) 1794771019

14. PAG 2015 GA12 Biosynthesis: Preliminary comparative view Os japonica Os indica O. rufipogon O. nivara A. thaliana Orthology Projections

15. PAG 2015 Ethylene Biosynthesis and Signaling: Comparative view Os japonica Os indica O. rufipogon O. nivara O. australiensis Orthology Projections The latest Reactome software allows us to make these interspecies comparisons directly in the pathway browser.

16. PAG 2015 Pathway Curation

17. PAG 2015 Ongoing rice curation Currently >200 curated rice pathways Notable signaling pathways in recent releases: Auxin signaling Brassinosteroid signaling

18. PAG 2015 Arabidopsis curation  Converted AraCyc 11 data was merged into Reactome’s main curation database  Arabidopsis curation began in March 2014  Curation, beyond describing pathways not found in other databases, focuses on updating pathway data to reflect most recent literature  To date, ~70 curated A.th. pathways in the central database (…and counting)

19. PAG 2015 Arabidopsis curation Xylan biosynthesis Arginine biosynthesis I Ethylene biosynthesis

20. PAG 2015 The New Reactome Platform

21. PAG 2015 New Reactome platform Adapting the new “Reactome 3” platform for the Plant Reactome… Pathway Browser

22. PAG 2015 New Reactome platform EBI-ATLAS baseline expression data

23. PAG 2015 New Reactome platform Public API (JSON, XML)

24. PAG 2015 New Reactome platform Analysis Tools: Upload data and analyze

25. PAG 2015 New Reactome platform Analysis Tools: O.sativa diurnal expression (time course)

26. PAG 2015 New Reactome platform Analysis Tools: Metabolomics data, too…

27. PAG 2015 New Reactome platform Species comparison: O. sativa to Z.mays

28. PAG 2015 Upcoming Gramene Webinar Other Upcoming Gramene Webinars 2 pm EST DateTopic February 10, 2015Overview of the Genome browser March 3, 2015Genome browser: Identify gene trees & homologs April 7, 2015 @ TBD*Rice resources in Gramene April 28, 2015Maize resources in Gramene May 19, 2015Genome browser: Upload and display your own data June 9, 2015Expression data analysis on plant Cyc pathways * Night time in the US to accommodate users from Asia, Australia, etc. January Webinar Gramene: Plant Reactome Justin Preece Tuesday, January 27, 2015 2:00 – 2:30 pm EST

29. PAG 2015 Many thanks to… Oregon State University  Vindhya Amarasinghe (Curation)  Sushma Naithani (Curation and outreach)  Justin Elser (Inparanoid pipeline)  Pankaj Jaiswal (Co-PI) Cold Spring Harbor Laboratory  Kapeel Chougule (Search integration)  Andrew Olson (Search integration) NYU Langone Medical Center  Peter D’Eustachio (Curation mentor) Ontario Institute for Cancer Research  Robin Haw (Server provision)  Joel Weiser  Sheldon McKay  Guanming Wu  Lincoln Stein (Reactome PI) European Bioinformatics Institute  Antonio Fabregat Mundo  Robert Petraszak (ATLAS integration)  Henning Hermjakob (Reactome, IntAct PI) Former Staff  Palitha Dharmawardhana (Ciuffetti Lab, OSU)  David Croft (EBI)  Ken Youens-Clark (Hurwitz Lab, U of Ariz.)  Hardeep Nahal (OICR)  Dylan Beorchia (OSU student curator)  Kindra Amoss (OSU student curator)