Transcript Ingenuity Pathway Analysis Alex Pico Description "IPA is a software

Ingenuity Pathway Analysis
Alex Pico
Description
"IPA is a software application that enables researchers
to analyze and understand the complex biological and
chemical systems at the core of life science research.
IPA integrates content from the world's largest and
highest quality knowledge base of biological and
chemical interactions, and employs powerful
algorithms and an easy to use software interface to
provide researchers with the insights and confidence
to make better and faster decisions at every step of
their research, from experimental planning to data
interpretation."
Basics
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Target Audience: Industry researchers in drug discovery
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Primary use cases:
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# Search and explore "the largest knowledge base of its kind with the most descriptive
structure, highest degree of accuracy, and largest number of literature findings."
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# Analyze and interpret data from expression and SNP arrays, proteomics and
metabolomics experiments, and small-scale experiments that generate gene lists. Grow
gene lists into pathways via the knowledge base using any combination of contextual,
annotation, or relationship information. Identify ideal biomarkers. Map experimental data
onto pathways (curated or home-grown). Use themed modules to study Metabolomics,
Toxicity, or Biomarkers.
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# Share and collaborate on analyses. Generate summary reports. Export results, tables of
annotations, bibliographies and high-res images. Utilize API, or deploy locally.
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Last updated: version 5.5 (sometime in the last few months)
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Platform: Web browser or standalone app on Vista, XP, Mac
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Plugin Architecture: API to integrate into local software pipeline. Integrated
with GeneSpring (Agilent), Resolver (Rosetta) and Spotfire
Features
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# The knowledge base is impressive in terms of both the model and content. This is
the sort of thing we could never hope to compete with as a non-profit consortium.
Though I can imagine an open, community-curated knowledge base that would, in
the end, produce a superior product, this is probably not a task for Cytoscape.
# Ingenuity is able to integrate a single knowledge base for gene ID aliases,
chemicals, drugs and small molecules, interactions, curated pathways, literaturebased relationships, and workflow-related annotations (e.g., biomarkers). This
singular, controlled source allows them to reference across multiple data types and
levels from different perspectives. While we may not be able to produce a knowledge
base, we can (and do) integrate public databases. It might be worth thinking about
how information from these sources can be integrated or cross-referenced within
Cytoscape. It may be equally worthwhile thinking about when sources should be
segregated or pruned to provide focus (e.g., biological semantics).
# Beyond the knowledge base, Ingenuity's most valuable qualities are the polished,
professional look and feel (including its new web interface) and its specialized
workflows and modules. Having focused workflows and perspectives brings to bear
specialized windows, menus, data types and integrated content that make the
application very user-friendly and effective.