august 29, 2002informax confidential1 vector pathblazer product overview
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August 29, 2002 InforMax Confidential 1
Vector PathBlazerVector PathBlazer
Product OverviewProduct Overview
August 29, 2002 InforMax Confidential 2
AgendaAgenda
• Introduction to Vector PathBlazer
• Product Features and Benefits
• Future Direction
August 29, 2002 InforMax Confidential 3
AgendaAgenda
• Introduction to Vector PathBlazer
• Product Features and Benefits
• Future Direction
August 29, 2002 InforMax Confidential 4
Vector Family of ProductsVector Family of Products
Vector PathBlazerVector PathBlazerVector XpressionVector Xpression
•Work with RNA quantitation
•Which genes are turned on or off under conditions of interest
•Gene and sample profiling
•Work with biological pathways and protein-protein interactions
•Add your own data to curated data
•Work with gene and protein sequence
•Understand sequence
•Classify genes based on sequence similarity
•Design sequences for wet lab experiments
VectorNTIVectorNTI
August 29, 2002 InforMax Confidential 5
Vector PathBlazerVector PathBlazer
Vector PathBlazer Vector PathBlazer is a powerful, easy to use and is a powerful, easy to use and flexible desktop application for analysis of flexible desktop application for analysis of biological pathwaysbiological pathways
Vector PathBlazer is the only tool that Vector PathBlazer is the only tool that makes it makes it easy to integrate pathway and interaction data easy to integrate pathway and interaction data from multiple sourcesfrom multiple sources
Vector PathBlazer Vector PathBlazer is supported by experienced is supported by experienced bioinformaticists, industry leading technical bioinformaticists, industry leading technical support and tutorialssupport and tutorials
Vector PathBlazer Vector PathBlazer is the best available software is the best available software solution for both beginners and experts in the field solution for both beginners and experts in the field of biological interactions and pathwaysof biological interactions and pathways
August 29, 2002 InforMax Confidential 6
Definition of a PathwayDefinition of a Pathway
• A pathway is a set of linked biological components interacting with each other over time to generate a biological effect
• They can be broken down into components making a reaction and reactions making a pathway
August 29, 2002 InforMax Confidential 7
Capabilities of ProductCapabilities of Product
• Integrate current pathway and protein-protein interaction data content from multiple curated data sources
• Annotate and add user’s own data• Create subsets of pathways, reactions, components that
are relevant and of interest – by subcellular location, organelle, species etc.
• Draw own pathways • View pathways in multiple ways and export easily to other
programs for editing and publication• Generate hypotheses by building
– New potential pathways– Cross species queries to predict potential networks
• Overlay expression data on top of pathway to see how it changes with condition
August 29, 2002 InforMax Confidential 8
Industry leading frameworkIndustry leading framework
• PETRI Nets as a Mathematical Model for Biological Pathways– http://www.daimi.aau.dk/PetriNets/
PETRI nets are graph-like structures, which are easily exploited to represent various relations and interconnections of interacting entities (substrates, proteins) in a metabolic/regulatory network.
August 29, 2002 InforMax Confidential 9
Powerful, Intuitive, FlexiblePowerful, Intuitive, Flexible• The only desktop tool that allows users to store,
visualize, edit, create their own reactions and pathways
• Compelling core functionality that integrates biological pathway and protein interaction data from multiple sources
• Create useful biological connections with sequence and expression data
• Speed up your research efforts with easy links to external information
August 29, 2002 InforMax Confidential 10
AgendaAgenda
• Introduction to Vector PathBlazer
• Product Features and Benefits
• Future Direction
August 29, 2002 InforMax Confidential 11
Workflows SupportedWorkflows Supported
• Import KEGG, DIP,BIND, user’s own data• Searching pathways, reactions and components
to find relevant data• Manage and visualize protein-protein interaction
data• Edit and annotate existing pathways with private
data• Build novel pathways by combining private data
with public data (hypotheses generation)• Map expression data onto an existing pathway,
relating biology to pathway
August 29, 2002 InforMax Confidential 12
Query toolQuery tool
• Search pathways, reactions, components to find relevant data
– Pathways, reactions and components can be annotated at multiple levels
– Annotations can be searched (find items in humans, find items in this tissue, came from this database, …)
– Subsets are created that allow user to save logical collections for later use
August 29, 2002 InforMax Confidential 13
Annotation wizardAnnotation wizard
Easily annotate Easily annotate components, components, reactions and reactions and pathwayspathways
August 29, 2002 InforMax Confidential 14
Build pathways and networksBuild pathways and networks
Build pathways Build pathways including data including data from user from user created subsets created subsets of curated dataof curated data
August 29, 2002 InforMax Confidential 15
Customize viewsCustomize viewsEasily Easily customize views customize views and export to and export to other other applications for applications for publicationpublication
August 29, 2002 InforMax Confidential 16
Gene Expression and PathwaysGene Expression and Pathways
• Gene expression data can have:– Time points
(time course)– Treated vs
non-treated– Disease vs
non-disease– Mutant
analysis• Map gene
expression data supplied in the specified file format
A
B
C
D
A
B
C
D
A
B
C
D
A
B
C
D
View differential gene expression in the context of pathways
August 29, 2002 InforMax Confidential 17
Datasets SupportedDatasets Supported
• Specific importers for KEGG, BIND, DIP ship with product
• User is required to obtain permission for download and use of data– BIND is free– KEGG, DIP are free to academic, not to
commercial
• Additional importers in development • Custom parsers can be written for users data
of interest
August 29, 2002 InforMax Confidential 18
KEGGKEGG
• KEGG data, how is it parsed?
Compounds
Synonyms
Chemical Formula
Enzymes
Name:
EC #:
Educts:
Products:
Reactions:
Genes:
Reactions
R00078: 4 C00023 + 2 C00001 C00007 + 4 C00080 + 4 C00023
(may have directionality, no enzyme)
Map
Pathway name:
Reaction#_EC# pair:
GIF file link:
A
BD
Ez Ez
DA
BEz Ez
directionality
Reaction file has bi-directional, then both forward and back stored
Reaction file uni-directional, confirm with Educts/Products
Confirmation not possible, reaction is bi-directional
pathway
August 29, 2002 InforMax Confidential 19
BIND AND DIPBIND AND DIP
• BIND 2.0 and DIP data, how is it parsed?BIND Interaction.xml
Component
Synonyms
Organism
Protein Class
Chemical Formula
A
B
dip20020616.xin
Component
Synonyms
Organism
Class = protein by default
Reaction type = PPI (protein-protein
interaction)
August 29, 2002 InforMax Confidential 20
AgendaAgenda
• Introduction to Vector PathBlazer
• Product Features and Benefits
• Future Direction
August 29, 2002 InforMax Confidential 21
Continuous ImprovementContinuous Improvement
• Natural language processing – leverage content from literature
• Enhanced graphics (ie, more templates)• API exposure to manipulate graphics• Simulation of pathways (how levels of
components change with time, graph theory)
• Compare pathway, find critical points in pathway (graph theory algorithms)
• Collaborative central data storage