PowerPoint-Präsentation - CSC

PowerPoint-Präsentation - CSC

Reactome A database of biological pathways David Croft Reaction Example 1: Enzymatic 2 06.02.20 Reactome: a database of biological pathways www.reactome.org Reaction Example 2: Transport 3 06.02.20 Reactome: a database of biological pathways www.reactome.org

Reaction Example 3: Signaling Dimerization Phosphorylation 4 06.02.20 Reactome: a database of biological pathways www.reactome.org output input output catalyst input catalyst catalyst

A Reactome Pathway input Compartment 5 06.02.20 Reactome: a database of biological pathways www.reactome.org output Reactome Data Model Events: Reactions Pathways Entities: Proteins Complexes

Small compounds Modulation: Inhibition Activation 6 06.02.20 Reactome: a database of biological pathways www.reactome.org Where Reactomes Data Comes From 7 Expert

Curator Reviewer (recruited) (staff) (recruited) Expert and curator create outline of new pathway Expert fills in details Curator enters information into database Reviewer (another expert) checks biological correctness 06.02.20 Reactome: a database of biological pathways www.reactome.org Projecting Reactions to Other Species I Human

A B C A B -P + ADP C A B -P + ADP + ATP Mouse A B + ATP Drosophila

A B 8 06.02.20 + ATP Protein not inferred Reactome: a database of biological pathways www.reactome.org C Reaction not inferred Projecting Reactions to Other Species II Human - manually curated Notch signaling Drosophila - electronically inferred

9 06.02.20 Reactome: a database of biological pathways www.reactome.org Coverage - Current 10 Apoptosis Cell cycle DNA repair

Transcription, mRNA processing, translation, posttranslational modification Signaling pathways (insulin, NOTCH, opioid, NGF, EGFR, FGFR) Hemostasis Metabolism (energy, amino acid, lipid, nucleotide, xenobiotic) HIV and Influenza lifecycles Neurotoxicity of botulinum toxins 06.02.20 Reactome: a database of biological pathways www.reactome.org Coverage - Planned Due before end-2007 11

Signaling pathways (PDGF, Rho GTPases II) Obesity pathways Cholesterol metabolism Epigenetics: RNAi pathway 06.02.20 Reactome: a database of biological pathways www.reactome.org Reactome by Numbers November 2007 12 Pathways

Reactions Proteins Complexes Literature references 06.02.20 Reactome: a database of biological pathways www.reactome.org 765 2241 2203 (~10% SwissProt human) 1711 3144 Reactome APIs API Remote access Firewall tunneling

Perl Yes No Java Yes No BioMart Yes Yes Web services Yes

Yes Full details of BioMart at: www.biomart.org 13 06.02.20 Reactome: a database of biological pathways www.reactome.org BioMart and Reactome: GUI http://www.reactome.org:5555/biomart/martview 14 06.02.20 Reactome: a database of biological pathways www.reactome.org BioMart and Reactome: Web Services http://www.reactome.org:5555/biomart/martservice?query=...

** Perl API also available ** 15 06.02.20 Reactome: a database of biological pathways www.reactome.org Reactome Team www.reactome.org Cold Spring Harbor Laboratory Gene Ontology Consortium

Ewan Birney Imre Vastrik Esther Schmidt Bijay Jassal Bernard de Bono David Croft Phani Vijay Garapati Lincoln Stein Peter D'Eustachio Lisa Matthews Gopal Gopinath Marc Gillespie Guanming Wu Suzanna Lewis Grants European Bioinformatics Institute 16

06.02.20 Reactome: a database of biological pathways www.reactome.org NHGRI # R01 HG002639 EU STRP, EMI-CD EBI Industry program Reactome Web Page Walkthrough David Croft Front Page www.reactome.org Navigator Search Species Starry-sky Top-level

pathways 18 06.02.20 Reactome: a database of biological pathways www.reactome.org Pathway www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109581 Event hierarchy Description Participants Export 19 06.02.20

Reactome: a database of biological pathways www.reactome.org Pathway Participants Key: ChEBI UniProt Compound Ensembl GO MIM KEGG UCSC EntRezMed 20 06.02.20 Reactome: a database of biological pathways www.reactome.org

Pathway Data Export xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xml:base="http://www.biopax.org/release/biopax-level2.owl#"> rdf:datatype="http://www.w3.org/2001/XMLSchema#string">BioPAX pathway converted from "Apoptosis" in the Reactome database.

/> rdf:resource="#Apoptotic_execution__phaseStep" /> Apoptosis Apoptosis P6316

P98170 Q15628 P55211 P55957 P10415 P19438 P48454 Q9BXH1 O43521 P55210 Q07817 Q96FJ2 P31946 21 06.02.20 Reactome: a database of biological pathways www.reactome.org Reaction

www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=74711 Reaction diagram Reactants, products, catalyst. 22 06.02.20 Reactome: a database of biological pathways www.reactome.org Bookmarking and Stable IDs Get stable ID history: Use this link to bookmark the reaction 23 06.02.20

Reactome: a database of biological pathways www.reactome.org SkyPainter Entering a List of Identifiers www.reactome.org/cgi-bin/skypainter2?DB=gk_current Usable identifiers: UniProt RefSeq Ensembl MIM Entrez Gene Affymetrix GO KEGG COMPOUND ChEBI 24 06.02.20 Reactome: a database of biological pathways www.reactome.org

SkyPainter Overrepresented Events Decreasing significance 25 06.02.20 Reactome: a database of biological pathways www.reactome.org SkyPainter Numeric Values (e.g. Expression) #ID P20248 P14635 Q01094 P08319 O95067 P12004 P30305 P16104

P33992 P35249 O94913 Q13415 Q15054 P30307 O75496 P49736 Q13243 P50613 O75419 P30304 O96017 P38398 P06730 P15927 P30038 P51530 P17174 P35250 26

06.02.20 Reactome: a database of biological pathways www.reactome.org value1 2.381255 2.078063 1.358003 1.274531 1.251352 1.031162 1.654142 1.274092 1.560363 1.185243 2.410139 1.085086 1.148979 2.270973 0.796653 0.998988

2.634955 1.466119 1.853295 0.863513 0.889464 1.068929 1.789461 0.89531 0.655572 1.060222 1.611088 0.58771 Download: www.ebi.ac.uk/systemssrv/mp/file-exchange/E-MEXP-345.txt Move focus SkyPainter - Coloring Broken! Zoom in Zoom out

E.g. zoom in 27 06.02.20 Reactome: a database of biological pathways www.reactome.org Simple Search 28 06.02.20 Reactome: a database of biological pathways www.reactome.org Download Database Interactions Textbooks

Local installation Data entry tools Web services API 29 06.02.20 Reactome: a database of biological pathways www.reactome.org Protein-Protein Interactions Types of derived interaction: 30

Direct complex Indirect complex Reaction Neighboring reaction 06.02.20 Reactome: a database of biological pathways www.reactome.org

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