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Instructions for Arabidopsis Reactome Authors Janet Higgins November 2008 [email protected] Contents 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. Workflow in Arabidopsis Reactome Reactome Data Model Types of Reaction Authoring a module Information required Formatting of the information in Word document Gene and reference list in Excel How to use Author Tool Author Tool – Graphic editor Author Tool – Property editor SBGN Author Tool – Graphic editor Example of Phosphorylation reaction in Reactome Example of Complex formation in Reactome Example of Transport in Reactome Example of Transcription in Reactome Example of Translation in Reactome Workflow for authoring and curation of pathways in Arabidopsis Reactome Author 1 Scientific expert Data Author tool Data Revise Data Curator tool Data and revisions Review Data Reactome curator Peer Review Arabidopsis Reactome (development) Arabidopsis Reactome (web) Reactome Data Model 2 Life on the cellular level is a network of molecular interactions. Molecules are synthesized and degraded, transported from one location to another, and form complexes with other molecules. Reactome represents all of this complexity as reactions in which input physical entities are converted to output entities as shown below Input 1 Reaction Output Input 2 Reactions are linked together by shared physical entities: a product from one reaction may be a substrate in another reaction and may catalyze another. Reactions are grouped into pathways (sets of interlinked reactions), pathways are grouped into larger pathways forming a hierarchical structure. 3 3. Types of Reaction Binding/complex formation A B Transcription Translation A mRNA A B Regulation Degradation Phosphorylation Dephosphorylation Transport A A A P A Cytosol Catalyst A Nucleus Authoring a module (Please refer to slide number in brackets) Make a list of genes in the pathway (7) and group them into separate mini-pathways. Collate the information (5 and 6) in a word document. Optional - Input your pathway using Author Tool (8-10). The Reactome Curator can use the information in a word document to input the pathway directly into Curator Tool. Make a list of references (7) used as experimental evidence for reactions and pathways. Slides 12 to 16 shows examples of different types of reaction showing the information required for each reaction. Please click on the links to see the reaction in Reactome 4 Information Required 5 1. The entities involved and what state they are in (ie dimer, phosphorylated etc) and their compartment 2. If applicable, the catalyst - composed of the actual entity with a GO molecular function ID assigned to it if available. 3. The compartment where this event takes place - we do allow adjacent compartments eg an entit in the cytosol binds to an entity in the plasma membrane 4. A PUBMED literature reference which defines the event, experimentally, in Arabidopsis. 5. IDs – AGI for proteins, ChEBI/KEGG IDs for small molecules, GO compartment IDs for compartments and GO molecular function IDs for mol function. Also, GO Biological Process terms for Pathways. 6. The organism - obviously we are working on Arabidopsis but if an event is described experimentally in another organism (and there are many examples of that), we create the event in that organism and link it to our Arabidopsis event, showing the homologs in Arabidopsis. 7. Summations – these are free text summaries we can add to pathways and reactions to give extr meaning to what is happening in that particular event. For pathways, we would expect a fairly substantial explanation of the pathway, for reactions we expect a short description of that reaction may be helpful. Format your information as shown below in a word document 1. NAME OF EVENT: Pathway eg Formation of CDKD:CYCH complex by CDK-activating kinase GO biological process: for pathways normally EVENT compartment: nucleoplasm GO:0005654 PubMed IDs: for pathways, reviews SPECIES: Arabidopsis thaliana SUMMATION: eg The CDK-activating kinase pathway involving CDKF and CDKD associated with CYCH is required for full activation of the CDKA/CYCD complex. 1.1 NAME OF EVENT: Reaction eg Formation of CDKD:CYCH complex EVENT compartment: eg nucleoplasm GO:0005654 PubMed IDs: for reactions, the experimental evidence SPECIES: Arabidopsis thaliana INPUT 1: eg Phospho-(Ser162,Thr168) CDKD;2 AT1G66750 INPUT 2: eg CYCH;1 AT5G26720 CATALYST: where applicable including GO molecular function OUTPUT: eg Phospho-(Ser162,Thr168) CDKD;2 :CYCH;1 complex SUMMATION: if more information will be helpful 6 7 Gene and Reference list in Excel Example of gene list Gene name Example of reference list AGI code author date subject PubMed PHYA AT1G09570 1 McClung 2006 History PHYB AT2G18790 2 Gardner 2006 review 16761955 PHYC AT5G35840 3 Locke 2005 BIOMD55 16729048 PHYD AT4G16250 4 Locke 2006 BIOMD89 17102804 PHYE AT4G18130 5 Zeilinger 2006 PRR7/9 17102803 CRY1 AT4G08920 6 Dodd 2005 growth 16040710 CRY2 AT1G04400 7 Covington 2007 auxin 17683202 8 Ding 2007 TIC 17496120 9 McWatters 2007 ELF4 17384164 8 How to use the Author Tool • Start Author Tool version 3.0 in Java Web Start from http://n55960/download/index.html • Add Objects by clicking on them in the Palette. • Join the objects together using the various options available. • Add detail in Property editor. • A user guide will be available later this year, if you have any questions email [email protected] The SBGN version of author tool can be accessed at http://brie8.cshl.org:8080/ReactomeTools/AuthorTool/authorToolLaunch.html Author Tool – Graphic Editor Produce Associate Phosphorylate Inhibit Activate Interact Encode 9 Author Tool – Property Editor 10 SBGN Author Tool – Graphic Editor Produce Associate Phosphorylate Inhibit Activate Interact Encode 11 Example of Phosphorylation 12 http://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&FOCUS_SPECIES=Arabidopsis%20thaliana&ID=47737& EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702 Phosphorylation of CDTa by CDKA/CYCD2;1 CDT1a AT2G31270 Phospho - CDT1a AT2G31270 nucleoplasm GO:0005654 nucleoplasm GO:0005654 Catalyst CDKA;1:CYCD2;1 complex PubMed Id 15316110 INPUT OUTPUT CDKA;1 CDKA;1:CYCD2;1 complex made up of AT2G48750 + CYCD2;1 AT2G22490 Example of Complex Formation 13 http://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&FOCUS_SPECIES=Arabidopsis%20thaliana&ID=47539& EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702 Phospho-(Ser162,Thr168) CDKD;2 AT1G66750 nucleoplasm GO:0005654 Formation of CDKD:CYCH Complex Phospho-(Ser162,Thr168) CDKD;2 :CYCH;1 complex nucleoplasm GO:0005654 CYCH;1 nucleoplasm GO:0005654 PubMed Id 16856985 AT5G26720 INPUT OUTPUT Example of Transport http://n55960/cgi-bin/eventbrowser?DB=test_reactome_9_ath_all&ID=47328& EVENT Arabidopsis thaliana NCBI taxonomy:3702 CDKA;1 AT1G66750 Transport of CDKA into the nucleus cytosol GO:0005654 AT1G66750 nucleoplasm GO:0005654 Regulated by ICK1 At2g23430 PubMed Id 16845478 CDKA;1 INPUT OUTPUT 14 15 Example of Transcription Example in developer copy of Reactome EVENT nucleoplasm GO:0005654 Arabidopsis thaliana NCBI taxonomy:3702 PubMed Id 15767265 Transcription of PRR5 regulated by CCA1 and LHY This is a black box reaction so it requires no input prr5 mRNA RefSeq:NM_122355 nucleoplasm GO:0005654 Positive or negative regulation CCA1 LHY AT2G46830 AT1G01060 OUTPUT Example of Translation Example in developer copy of Reactome EVENT cytosol GO:0005829 Arabidopsis thaliana NCBI taxonomy:3702 PubMed Id Translation of mRNA to PRR5 protein 15767265 prr5 mRNA PRR5 RefSeq:NM_122355 AT5G24470 cytosol GO:0005829 cytosol GO:0005829 INPUT OUTPUT 16