Vector PathBlazer Product Overview

1
Vector PathBlazerProduct Overview
2
Agenda

• Introduction to Vector PathBlazer
• Product Features and Benefits
• Future Direction

3
Agenda

• Introduction to Vector PathBlazer
• Product Features and Benefits
• Future Direction

4
Vector Family of Products
Vector PathBlazer
Vector Xpression
VectorNTI

• 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

5
Vector PathBlazer

• Vector PathBlazer is a powerful, easy to use and
  flexible desktop application for analysis of
  biological pathways
• Vector PathBlazer is the only tool that makes it
  easy to integrate pathway and interaction data
  from multiple sources
• Vector PathBlazer is supported by experienced
  bioinformaticists, industry leading technical
  support and tutorials
• Vector PathBlazer is the best available software
  solution for both beginners and experts in the
  field of biological interactions and pathways

6
Definition 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

7
Capabilities of Product

• Integrate current pathway and protein-protein
  interaction data content from multiple curated
  data sources
• Annotate and add users 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

8
Industry 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.

9
Powerful, 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

10
Agenda

• Introduction to Vector PathBlazer
• Product Features and Benefits
• Future Direction

11
Workflows Supported

• Import KEGG, DIP,BIND, users 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

12
Query 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

13
Annotation wizard
Easily annotate components, reactions and pathways
14
Build pathways and networks
Build pathways including data from user created
subsets of curated data
15
Customize views
Easily customize views and export to other
applications for publication
16
Gene 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

View differential gene expression in the context
of pathways
17
Datasets 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

18
KEGG

• KEGG data, how is it parsed?

Compounds Synonyms Chemical Formula
Reactions R00078 4 C00023 2 C00001 ? C00007
4 C00080 4 C00023 (may have directionality, no
enzyme)
Enzymes Name EC Educts Products Reactions G
enes
Ez
Ez
A
Map Pathway name Reaction_EC pair GIF file
link
D
B
pathway
A
directionality Reaction file has bi-directional,
then both forward and back stored Reaction file
uni-directional, confirm with Educts/Products Conf
irmation not possible, reaction is bi-directional
D
B
Ez
Ez
19
BIND AND DIP

• BIND 2.0 and DIP data, how is it parsed?

BIND Interaction.xml Component Synonyms Organism P
rotein Class Chemical Formula
A
B
Reaction type PPI (protein-protein interaction)
dip20020616.xin Component Synonyms Organism Class
protein by default
20
Agenda

• Introduction to Vector PathBlazer
• Product Features and Benefits
• Future Direction

21
Continuous 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

22
Contact

• Register for a tour of Vector PathBlazer today!
• http//www.informaxinc.com/solutions/
• System Requirements
• Windows 98, 2000, NT, ME and XP platforms
• 64MB RAM needed, 128MB recommended
• 1GB HD disc space
• Internet connection