June Welcome - webinar instructions All microphones will be muted whilst the trainer is speaking At the end of the presentation, we will take questions via the chat at the bottom of the GoToTraining panel. If you wish to ask a question, please use the “raise your hand” button and we can open your microphone. Please complete the feedback survey which will launch at the end of the webinar.
Webinar June 2016 The Reactome Pathway Database Steve Jupe
June Overview Introduction Data Curation and Content Tools Pathway Browser Analysis Tools Summary Acknowledgements
June Rationale – Journal information Nature 407(6805):770-6.The Biochemistry of Apoptosis. “Caspase-8 is the key initiator caspase in the death-receptor pathway. Upon ligand binding, death receptors such as CD95 (Apo-1/Fas) aggregate and form membrane- bound signalling complexes (Box 3). These complexes then recruit, through adapter proteins, several molecules of procaspase-8, resulting in a high local concentration of zymogen. The induced proximity model posits that under these crowded conditions, the low intrinsic protease activity of procaspase-8 (ref. 20) is sufficient to allow the various proenzyme molecules to mutually cleave and activate each other (Box 2). A similar mechanism of action has been proposed to mediate the activation of several other caspases, including caspase-2 and the nematode caspase CED-3 (ref. 21).” How can I access the pathway described here and reuse it?
June Nature Oct 12;407(6805): The biochemistry of apoptosis. Rationale - Figures “A picture paints a thousand words…” but… Not data, just pixels Omits key details Assumes familiarity Fact or hypothesis?
June What is Reactome? Free open source human pathway knowledgebase Normal and disease-related pathways Mapped to cellular compartments Every event supported by published experiments (with citations). Authored by expert biologists, maintained by professional Curators Tools for data analysis and visualization Understanding gene lists or expression data in pathway context Downloads and RESTful API to support Computational Biology
June Why Reactome? Reactions Pathway steps = Units of Reactome = biological event TRANSPORT CLASSIC BIOCHEMICAL BINDING DISSOCIATION DEGRADATION PHOSPHORYLATION DEPHOSPHORYLATION
June Primary Sources (cross references) UniProt – proteins ChEBI – small molecules Ensembl – genes and transcripts RNA Central - ncRNAs PubMed – literature evidence GO Molecular Function Compartment Biological process
June Reaction example 1: Enzymatic
June Reaction example 2: Transport R-HSA Transport of Ca++ from platelet dense tubular system to cytoplasm
June Other reaction examples Binding Dimerization Phosphorylation
June Reactions connect into Pathways OUTPUT INPUT CATALYST OUTPUT INPUT CATALYST INPUT OUTPUT CATALYST
June Human pathway PMID:5555PMID:4444 mouse cow Direct evidence Indirect evidence PMID:8976 PMID:1234 Evidence – Inferred Reactions
June Pathways authored and reviewed by expert biologists Curator works with Author to represent knowledge in Reactome data structure New pathways sent for review by another expert New data release every 3 months Regular pathway updates. ORCID and used as attributions for Reactome content –For visibility of expert contributions (authors, reviewers and curators). Data Curation Process Curator ExpertReviewer
June Species Selection
June Data Expansion – Projecting to Other Species A + ATP A + ADP -P B Human A + ATP A + ADP -P B Mouse B A Drosophila Reaction not projected No orthologue - Protein not projected + ATP
June Disease annotation in Reactome Three main areas: Infection (eg. HIV, influenza, botulism) microbially-expressed proteins Cancer (eg. EGFR, FGFR and NOTCH signalling) altered protein functions Metabolic diseases (eg. mucopolysaccharidoses, phenylketonuria, vitamin metabolism abnormalities) altered expression of proteins
June Disease display in Reactome - Infection Host Interactions of HIV factors
June Disease display in Reactome – Altered protein function in Cancer Constitutive Signaling by AKT1 E17K in Cancer
June Disease display in Reactome – Loss of function in metabolism MPS IIID - Sanfilippo syndrome D
June Downloads Pathways from Pathway Browser as text, PDF, etc. Entire database contents (and software) from Downloads page (linked to Homepage). Reusable standard formats BioPAX SBML UniProt to Pathways GO annotations Protein-Protein interaction pairs - Interactions between proteins in the same complex, reaction, or adjoining reaction
June Contents Version 56 has annotations for: 9238 human proteins, 9422 complexes ~1800 small molecules, 9584 reactions, 2007 pathways, ~20,000 literature references.
June Coverage – Content, TOC And many more...
June Planned Coverage – Editorial Calendar
June Reactome Tools Interactive Pathway Browser Analysis Over-representation Pathway topology Expression overlay Molecular interaction overlay Species comparison
June Front Page
June Search Reactome
June Search Reactome II
June Search Reactome III
June Search Reactome IV
June Search Reactome V
June The Pathway Browser HomeSpecies Layout Hierarchy Panel Thumbnail Zoom/Move Pathway Panel Detail Panel Fit to Page Open Diagram Video Tour Settings
June Pathway Overview 33
June Hierarchy Panel Pathway Reaction Black-box Inferred from New Updated Disease
June The Pathway Browser - Pathway Diagrams Ovals are small molecules (or sets of) Green boxes are proteins, Blue are complexes, Blue with double-boundary are sets Transition Binding Dissociation Omitted Uncertain Regulation +ve -ve Catalyst Inputs Outputs Compartment Reaction node
June Navigating in the Pathway Browser I Details here Home button Click reaction to open Click pathway to select, double-click to open diagram
June Subpathway Highlighting
June Details don’t update until selection Navigating in the Pathway Browser II Hover mouse HighlightsSelected
June Navigating in the Pathway Browser III
June Contextual Information Panel Names/IDsPin/Unpin
June Interactors Click for Interactors Slide to FilterDownloadClick edge for evidence
June Diagram Search
June Colour Profiles
June Diagram Key
June Export Diagram
June Show Illustration
June The Details Panel - Overview Select Reveal Details Background Orthologues Key literature Before & After
June
June Disease in Reactome Click here to display disease reaction Disease reaction overlaid on normal pathway Disease details
June The Big List of Differentially Pathways and Experiment Expressed Molecules beyond….. Interpreting high-throughput data…Reactome Tools
June Analysis
June Analysis submission (identifier lists)
June Analysis of identifier lists - Options
June Analysis Result – Over-representation FDR
June Analysis - Pathway topology matching
June Expression overlay I
June Expression overlay II Scaled to Data Step through Data columns Selected
June Species Comparison I
June Species Comparison II Yellow = orthologue No colour = not found OR no data
June Molecular Interaction Overlay Click line… Zoom
June Molecular Interaction Overlay - Data
June Molecular Interaction Overlay – Set source
June More Information From the Reactome Homepage Reactome User Guide Tour Train Online -
June Conclusions Reactome is a curated database of human biological pathways. Web site provides tools for visualizing and interpreting your experimental data. Downloadable as a data framework for systems biology modeling. All Reactome data and software are open, no licensing is required.
June Acknowledgements
June Thank you Questions, comments and suggestions