Copyright OpenHelix. No use or reproduction without express written consent1
IntAct IntAct: a database & analysis tools for protein interaction data Materials prepared by: Cynthia Foote, Ph.D. Cynthia Perreault-Micale, Ph.D. Updated: Q Version 2.0
Copyright OpenHelix. No use or reproduction without express written consent3 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct:
Copyright OpenHelix. No use or reproduction without express written consent4 Focus: protein interactions Interaction types: Valuable for cellular function & mapping signaling pathways IntAct Captures Protein Interaction Data A B Protein-Protein A Ca++ Protein-Small molecule Protein-Nucleic Acid A
Copyright OpenHelix. No use or reproduction without express written consent5 Sources & Organization of Interaction Data Curated interaction data from literature and direct user submissions Various experimental techniques used for determination The Data Model includes 3 levels of organization: Experiment Interaction Interactor
Copyright OpenHelix. No use or reproduction without express written consent6 IntAct Utilizes Controlled Vocabularies Controlled vocabularies ensure consistency and searchability For more details, see IntAct Help or OpenHelix introductory tutorials on Controlled Vocabularies or the Gene Ontology details
Static network views - Graph tab Copyright OpenHelix. No use or reproduction without express written consent7 View Protein Interactions Graphically Node Interconnecting lines Interactive network views - Cytoscape Control Panel Optional Network Panel Results Panel Data Panel - Attribute Browser Options Network View
Copyright OpenHelix. No use or reproduction without express written consent8 Many Homepage Features Highlighted data Tool bar open source software EMBL-EBI Introduction Statistics News examples
9 Search Options, Tools & Help Basic search with help Copyright OpenHelix. No use or reproduction without express written consent
10 Credits Developed by the Proteomics Services team at EBI, led by Henning Hermjakob Part of Protein and Nucleotide Database Group (PANDA), led by Rolf Apweiler and Ewan Birney Funding from a EU FELICS grant, other EU grants Collaborations: Shanghai Institutes for Biological Sciences AstraZeneca
Copyright OpenHelix. No use or reproduction without express written consent11 Publications & Citation Information Homepage left tool bar
Copyright OpenHelix. No use or reproduction without express written consent12 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct:
Copyright OpenHelix. No use or reproduction without express written consent13 IntAct Basic Search From Homepage Tpx2 More advanced searches can also be performed
Copyright OpenHelix. No use or reproduction without express written consent14 Basic Search Results Tabs Our query Query details Help for this view Options Click Magnifying glass for Interaction Details
Copyright OpenHelix. No use or reproduction without express written consent15 Basic Search Results - Interactions View Aliases Protein Names & Links Interaction Method & Accession Protein Species Publication Info. Expansion Method Molecule Type, i.e., protein Component, i.e., bait, prey, neutral Role, i.e., unspecified, inhibitor, ect.
Basic Search Results - Browsing Copyright OpenHelix. No use or reproduction without express written consent16 Click here
Basic Search Results - Lists View Copyright OpenHelix. No use or reproduction without express written consent17 Check all, one or several Choose an action for your selections Subtabs for molecule types
Copyright OpenHelix. No use or reproduction without express written consent18 Interaction Details Click Magnifying glass to reach Interaction Details Show all interactions Find similar interactions Experiment details Publication details Interaction details Click on any Dasty2 logo to reach Molecule View tab
Molecule View - Dasty2 Visualization Copyright OpenHelix. No use or reproduction without express written consent19 Mouse over Toggle open Protein features projected onto sequence & structure, if available BLAST
Copyright OpenHelix. No use or reproduction without express written consent20 Accessing Graphical Networks Click here to view graphical network Graph tab only active if less than 300 binary interactions Install Cytoscape locally to view a larger number of interactions (
Copyright OpenHelix. No use or reproduction without express written consent21 Static Graphical Networks A static network view Click here to open interactive view with Cytoscape Click here to download Cytoscape
Copyright OpenHelix. No use or reproduction without express written consent22 Interactive Graphical Networks - Cytoscape ↔ Control Panel Optional Network Panel Network View Results Panel Data Panel - Attribute Browser ↔ Options Help
Cytoscape Help is Available Copyright OpenHelix. No use or reproduction without express written consent23 Cytoscape User Manual
Copyright OpenHelix. No use or reproduction without express written consent24 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct:
Copyright OpenHelix. No use or reproduction without express written consent25 Advanced Search Access Click here Or click here Select Advanced Search from homepage tool bar Or click the upper Search tab
Copyright OpenHelix. No use or reproduction without express written consent26 Advanced Search Query Page Brca2
Copyright OpenHelix. No use or reproduction without express written consent27 Many results An Advanced Search Example two hybrid Select Boolean Operator Select Field Enter term Click here Our new query Fewer & more specific results Add additional search terms Select Organism, Enter Human
Copyright OpenHelix. No use or reproduction without express written consent28 Additional Advanced Searching Methods Catalase activity # of matching interactions
Chemical Search Copyright OpenHelix. No use or reproduction without express written consent29 Combine search terms Search by Substructure, Similarity or Identity Draw your molecule or select a template link export
Copyright OpenHelix. No use or reproduction without express written consent30 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct:
Copyright OpenHelix. No use or reproduction without express written consent31 MiNe – Minimal Connecting Interaction Network Web-based application which computes the minimal connecting network for a given set of proteins, if possible Results are forwarded to Hierarch View to visualize Maximum number of proteins allowed is seven Click here Homepage left tool bar
Copyright OpenHelix. No use or reproduction without express written consent32 MiNe Homepage Introduction Application details Search phrases Enter search phrase EBI-1389, EBI-1765
Copyright OpenHelix. No use or reproduction without express written consent33 MiNe Results Results are displayed in the Hierarch View window Ontology window Don’t use
Copyright OpenHelix. No use or reproduction without express written consent34 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct:
Copyright OpenHelix. No use or reproduction without express written consent35 Additional Features 1. Downloading 2. Third party network visualization software 3. Targets application
Copyright OpenHelix. No use or reproduction without express written consent36 Data Downloading PSI-MI is an XML format supported by the Human Proteome Organisation for storing and exchanging molecular interaction data Allows data to be held in multiple files which can be amalgamated On homepage Interactions view
Copyright OpenHelix. No use or reproduction without express written consent37 Data Download from Interactions View Open “Export to:” dropdown menu Select a format & click “Export”
Copyright OpenHelix. No use or reproduction without express written consent38 Data Download from Hierarch View - MiNe Tool From Hierarch View select PSI-MI TAB or PSI-MI 2.5 button on left side of window Click here
Copyright OpenHelix. No use or reproduction without express written consent39 PSI-MI 2.5 File XML file window opens Import into third party software
Copyright OpenHelix. No use or reproduction without express written consent40 Third Party Visualization Software Cytoscape- visualizes molecular interaction networks and integrates with gene expression data PIMWalker- an interactive tool for displaying protein interaction networks Categorie/PIMWALKER.html ProViz- allows for selecting of proteins by Gene Ontology Annotations but runs exclusively on the Linux operating system platform Access also directly from Graphs view Access also directly from Tools menu
Copyright OpenHelix. No use or reproduction without express written consent41 Targets Access Targets in Tools section of homepage An application to predict targets for pull-down experiments Click here Homepage left tool bar
Copyright OpenHelix. No use or reproduction without express written consent42 Predicting Targets for Pull-Down Experiments Click here
Copyright OpenHelix. No use or reproduction without express written consent43 Predicted Targets – Results RankedLinked
Copyright OpenHelix. No use or reproduction without express written consent44 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct:
Copyright OpenHelix. No use or reproduction without express written consent45 IntAct - A Protein Interaction Database System Tpx2 Catalase activity Basic & Advanced Search Tools
Copyright OpenHelix. No use or reproduction without express written consent46 Detailed Results & Access to Many Tools Help is easy to find & use Many additional tools available
Static network views - Graph tab Copyright OpenHelix. No use or reproduction without express written consent47 Visualize & Manipulate Protein Interaction Networks Node Interconnecting lines Customize your network view Interactive network views - Cytoscape A plethora of research applications
Copyright OpenHelix. No use or reproduction without express written consent48 IntAct Agenda Introduction & Credits Basic Search & Results Advanced Search MiNe Tool Additional Features Summary Exercises IntAct:
Copyright OpenHelix. No use or reproduction without express written consent49