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A database of biological pathways David Croft Reactome.

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1 A database of biological pathways David Croft Reactome

2 Reactome: a database of biological pathways www.reactome.org 27.02.082 History Started off as Genome Knowledgebase (GKB) spring 2001 Initially tried to capture and standardize the language used to describe molecular processes 2001/2002 realized that what we are trying to capture are reactions and pathways Re-branded as Reactome June 2004

3 Reactome: a database of biological pathways www.reactome.org 27.02.083 Reaction Example 1: Enzymatic

4 Reactome: a database of biological pathways www.reactome.org 27.02.084 Reaction Example 2: Transport

5 Reactome: a database of biological pathways www.reactome.org 27.02.085 Reaction Example 3: Signaling Dimerization Phosphorylation

6 Reactome: a database of biological pathways www.reactome.org 27.02.086 A Reactome Pathway inputoutput catalyst inputoutput catalyst inputoutput catalyst Compartment

7 Reactome: a database of biological pathways www.reactome.org 27.02.087 Reactome Data Model Events: Reactions Pathways Entities: Proteins Complexes Small compounds Modulation: Inhibition Activation

8 Reactome: a database of biological pathways www.reactome.org 27.02.088 Reactome Data Model – The Awful Truth

9 Reactome: a database of biological pathways www.reactome.org 27.02.089 Where Reactome’s Data Comes From Expert and curator create outline of new pathway Expert fills in details Curator enters information into database Reviewer (another expert) checks biological correctness Curator (staff) Expert (recruited) Reviewer (recruited)

10 Reactome: a database of biological pathways www.reactome.org 27.02.0810 Release cycle Repository Release DB Extract finished & reviewed topics Computationally project pathways to other organisms Add useful cross-references (ENSEMBL, UniProt, etc.) www.reactome.org Not publicly accessible

11 Reactome: a database of biological pathways www.reactome.org 27.02.0811 Links to External Databases BROAD KEGG COMPOUND ChEBI Dictybase EC EMBL ENSEMBL Entrez EntrezGene Flybase GO (function, process, compartment) HapMap IntAct KEGG Gene MIM PubChem Compound PubChem Substance RefSeq SGD UCSC UniProt Wormbase

12 Reactome: a database of biological pathways www.reactome.org 27.02.0812 Links out from Reactome GO molecular function Compartment biological process KEGG compound Chebi UniProt PubMed

13 Reactome: a database of biological pathways www.reactome.org 27.02.0813 Projecting Reactions to Other Species I A + ATP A + ADP -P B Human A + ATP A + ADP -P B Mouse BA Drosophila Reaction not inferred Protein not inferred + ATP

14 Reactome: a database of biological pathways www.reactome.org 27.02.0814 Projecting Reactions to Other Species II Notch signaling Human - manually curated Drosophila - electronically inferred

15 Reactome: a database of biological pathways www.reactome.org 27.02.0815 Protein-Protein Interactions Types of derived interaction: Direct complex Indirect complex Reaction Neighboring reaction

16 Reactome: a database of biological pathways www.reactome.org 27.02.0816 Coverage - Current Apoptosis Cell cycle DNA repair Transcription, mRNA processing, translation, post- translational modification Signaling pathways (insulin, NOTCH, opioid, NGF, EGFR, FGFR, Rho GTPases II, Opioid) Hemostasis Metabolism (energy, amino acid, lipid, nucleotide, xenobiotic) Synaptic transmission Lipoproteins – HDL and VLDL

17 Reactome: a database of biological pathways www.reactome.org 27.02.0817 Coverage - Planned Regulation of Insulin Norepinephrine &Serotonin Neurotransmitter Release Cycles GPCR signaling Axonal guidance Due by Summer 2009

18 Reactome: a database of biological pathways www.reactome.org 27.02.0818 Reactome by Numbers Pathways 960 Reactions 3203 Proteins 3702(~14% SwissProt human) Complexes 2583 Literature refs 4769 June 2009

19 Reactome: a database of biological pathways www.reactome.org 27.02.0819 Reactome APIs Yes Web services Yes BioMart NoYesJava NoYesPerl Firewall tunnelingRemote accessAPI Full details of BioMart at: www.biomart.org

20 Reactome: a database of biological pathways www.reactome.org 27.02.0820 BioMart Dataset PK FK Pathway Protein Full details of BioMart at: www.biomart.org Gene Small molecule

21 Reactome: a database of biological pathways www.reactome.org 27.02.0821 BioMart Advantages Query without needing to know data model Scales for big datasets Easy linking to other Marts (federation)

22 Reactome: a database of biological pathways www.reactome.org 27.02.0822 BioMart and Reactome: Datasets Main tables: Complex Pathway Reaction Interaction Dimension tables: Gene Protein Small Molecule Literature reference

23 Reactome: a database of biological pathways www.reactome.org 27.02.0823 BioMart and Reactome: GUI

24 Reactome: a database of biological pathways www.reactome.org 27.02.0824 BioMart and Reactome: Web Services http://www.reactome.org:5555/biomart/martservice?query=... ** Perl API also available **

25 Reactome: a database of biological pathways www.reactome.org 27.02.0825 BioModels A repository of curated biological models Models obtained from submissions, literature & collaborations Two-way linking with Reactome www.ebi.ac.uk/biomodels

26 Reactome: a database of biological pathways www.reactome.org 27.02.0826 The Team CSHL/OICR Lincoln Stein (PI) Gopal Gopinath, Marc Gillespie, Bruce May, Mike Caudy, Jill Hemish (curators) Guanming Wu, Alexander Kanapin (developers) EBI Ewan Birney, Henning Hermjakob (co-PIs) Esther Schmidt, Imre Vastrik, David Croft, Gavin O’Kelly (developers) Bernard de Bono, Bijay Jassal, Phani Vijay Garapati, Steven Jupe (curators) NYU Peter D’Eustachio (co-PI; editor-in-chief) Lisa Matthews (curator) Shahana Mahajan (curator) NHGRI P41 HG003751 EU STRP, EMI-CD EBI Industry program Grants

27 Tutorial David Croft Reactome

28 Reactome: a database of biological pathways www.reactome.org 27.02.0828 Front Page www.reactome.org Navigator Search Species Starry-sky Top-level pathways

29 Reactome: a database of biological pathways www.reactome.org 27.02.0829 Exercise 1

30 Reactome: a database of biological pathways www.reactome.org 27.02.0830 How to Search Rectome

31 Reactome: a database of biological pathways www.reactome.org 27.02.0831 Customizing Search Results Put all results on one web page (i.e. no pagination) Select the type of result you would like to see

32 Reactome: a database of biological pathways www.reactome.org 27.02.0832 Exercise 2

33 Reactome: a database of biological pathways www.reactome.org 27.02.0833 Pathway Event hierarchy Description Participants Export www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109581

34 Reactome: a database of biological pathways www.reactome.org 27.02.0834 Exercise 3

35 Reactome: a database of biological pathways www.reactome.org 27.02.0835 Reaction diagram Reactants, products, catalyst. www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=74711

36 Reactome: a database of biological pathways www.reactome.org 27.02.0836 Exercise 4

37 Reactome: a database of biological pathways www.reactome.org 27.02.0837 Protein www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=70597 Links to other databases Cellular compartment Posttranslational modifications

38 Reactome: a database of biological pathways www.reactome.org 27.02.0838 Exercise 5

39 Reactome: a database of biological pathways www.reactome.org 27.02.0839 SkyPainter – Numeric Values (e.g. Expression) #IDvalue1 P202482.381255 P146352.078063 Q010941.358003 P083191.274531 O950671.251352 P120041.031162 P303051.654142 P161041.274092 P339921.560363 P352491.185243 O949132.410139 Q134151.085086 Q150541.148979 P303072.270973 O754960.796653 P497360.998988 Q132432.634955 P506131.466119 O754191.853295 P303040.863513 O960170.889464 P383981.068929 P067301.789461 P159270.89531 P300380.655572 P515301.060222 P171741.611088 P352500.58771 … Download: www.ebi.ac.uk/systems- srv/mp/file-exchange/E-MEXP- 345_Reactome.txt Usable identifiers: UniProt RefSeq Ensembl MIM Entrez Gene Affymetrix GO KEGG COMPOUND ChEBI

40 Reactome: a database of biological pathways www.reactome.org 27.02.0840 SkyPainter – expression data display Step through, stop/start dataset display Toggle pathway names

41 Reactome: a database of biological pathways www.reactome.org 27.02.0841 SkyPainter – Overrepresented Events Decreasing significance

42 Reactome: a database of biological pathways www.reactome.org 27.02.0842 Exercise 6

43 Reactome: a database of biological pathways www.reactome.org 27.02.0843 BioMart – selecting your dataset

44 Reactome: a database of biological pathways www.reactome.org 27.02.0844 BioMart – filters

45 Reactome: a database of biological pathways www.reactome.org 27.02.0845 BioMart – attributes Check to get attribute

46 Reactome: a database of biological pathways www.reactome.org 27.02.0846 BioMart – results

47 Reactome: a database of biological pathways www.reactome.org 27.02.0847 Exercise 7

48 Reactome: a database of biological pathways www.reactome.org 27.02.0848 Reactome Links to BioModels Links to BioModels

49 Reactome: a database of biological pathways www.reactome.org 27.02.0849 BioModels Web Page Online simulation

50 Reactome: a database of biological pathways www.reactome.org 27.02.0850 JWS Simulation Parameters & initial concentrations Run the model

51 Reactome: a database of biological pathways www.reactome.org 27.02.0851 Exercise 8

52 Reactome: a database of biological pathways www.reactome.org 27.02.0852 Other Reactome features Editorial Calendar (navigation bar  Content) Extended search (navigation bar  Tools) PathFinder (navigation bar  Tools)

53 Reactome: a database of biological pathways www.reactome.org 27.02.0853 The End.

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