Transcript Intro to IPA

Ingenuity Pathways Analysis v5.5
Adam Corner, PhD ([email protected])
Agenda
• Introduction to Ingenuity
• Sample Studies:
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–
–
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IPA in Biomarker Discovery Research
IPA in Copy Number/Disease Mechanism Research
IPA in Metabolic Disorders
IPA in Metabolomics & Molecular Toxicology
Ingenuity Systems
•
Partial Customer List
Ingenuity Systems is the leading provider of
products and services that enable analysis
and exploration of biological data
– There is more data to analyze and explore
then there is time or resources
– Need to understand biological systems at
molecular, cellular and organismal level
– Essential to have the right content and tools
for the job
•
User base reflects strong adoption in
research community
– Top pharmaceutical companies
– Large biotechs
– Academic and government research labs
Discover the Biology
3
The Challenge
Data Analysis Across Multiple Dimensions of Biology
Systematic Generation of Novel
Biological and Therapeutic Insights
Disease
Processes
Cellular
Processes
Find genes
implicated in
disease
Cancer
Identify related cellular
processes, pathways
Apoptosis
Angiogenesis
Molecules
Fas
Vegf
Experimental
Platforms
Generate hypothesis
of molecular
mechanism
Informed in vivo, in
vitro assays
Discover the Biology
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The Challenge
Data Analysis Across Multiple Dimensions of Biology
Systematic Generation of Novel
Biological and Therapeutic Insights
Drug Induced
Injury/Pathology
Disease
Processes
Cellular
Processes
Cancer
Toxicological
Responses
Apoptosis
Angiogenesis
Xenobiotic Insult
Molecules
Fas
Vegf
Experimental
Platforms
Drug Treatment
Discover the Biology
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The Solution:
Ingenuity Pathways Analysis
Value
Solution
IPA is a software application that
enables researchers to analyse &
understand the complex biological
and chemical systems at the core
of life science research
Discover the Biology
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Discovery
Providing Value Throughout
Drug Discovery & Development Process
Understand disease
processes, identify
and validate targets
Biomarkers
Identify novel
biomarkers,
understand their
role in disease
pathways
Toxicology
Identify potential
mechanism of
toxicity
Pharmacogenomics
Gain insight into
differential
response to
therapeutics
Discover the Biology
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Ingenuity Publications
Peer-Reviewed Research Articles Citing IPA
600
528
Total # of Citations
500
400
300
200
100
0
2003
2004
2005
2006
through
September 2007
Full bibliography available at www.ingenuity.com
The Ingenuity Platform
Ingenuity Pathways
Knowledge Base
Ontology and Knowledge
Infrastructure
Client Solutions
Ingenuity Pathways
Analysis
Portal & Enterprise
Search Enablement
• ~ 1.8 million findings
manually extracted from full
text
• ~160 curated metabolic and
cell signaling pathways
• Chemical and drug info
• Signatures
• Scalable best-in-class
Content Acquisition
processes
Specialist Analytics
• Ingenuity Ontology of ca. 600,000
biological objects and processes in 12
major branches
• Robust, up-to-date synonym library
• Knowledge Infrastructure tools and
processes for structuring biological
and chemical knowledge
Enterprise KM Infrastructure
9
Ingenuity Pathways Knowledge Base
Database that is the core of Ingenuity’s Solutions
• The IPKB is a database that houses the most
context-rich, high quality content available
• Expert Extraction from full text of journals
•
•
Current coverage of ~300 journals, plus review
articles and textbooks
Manually extracted by trained Ph.D. scientists
• Biological Database Import:
•
OMIM, GO, EntrezGene
• Internally curated knowledge:
•
•
Signaling & Metabolic Pathways
Drug/Target/Disease relationships
• All findings structured for computation
•
Ingenuity Ontology covers protein, gene, protein
complex, cell, cellular component, tissue, organ,
small molecule & disease concepts and their
interrelationships
Simple Data Upload Process
• Flexible upload
process
eliminates time
consuming file
formatting steps
• Supports
analysis of id
lists with mixed
identifiers
•Array identifiers
•Gene identifiers
•Protein
identifiers
•Metabolomic
identifiers
• Stream lined
workflows
through 3rd
Party vendors
• API capabilities
Discover the Biology
14
Agenda
• Introduction to Ingenuity
• Sample Studies:
–
–
–
–
IPA in Biomarker Discovery Research
IPA in Copy Number/Disease Mechanism Research
IPA in Metabolic Disorders Research
IPA in Metabolomics & Mol. Toxicology Research
IPA in Biomarker Discovery
Research
• Goal of study: Identify diagnostic biomarkers for RA from rat transcriptomic
and human proteomic data
• Results: multiple inflammatory pathways are perturbed across all data sets
(Toll Like receptor signaling and IL6 & IL10 signaling). Multiple genes
associated with chemotaxis of leukocytes upregulated in both mRNA and
protein levels. Putative biomarkers supported by previous experimental data
findings e.g CCL5
• Specific bottleneck addressed by IPA: Anchoring of molecular profiles to
phenotypes associated with RA. Integration of data from multiple platforms
(transcriptomic and proteomic) and disease models (CIA in rat & Erosive RA
in humans). Confirmation that putative biomarkers identified are available in
suitable biofluids.
Genomics data
Species: rat
Several pathways are commonly
perturbed across multiple datasets –
including IL-6 signaling, IL-10 signaling
and Toll-like receptor signaling.
Do known phenotypes e.g leukocyte
counts in Erosive RA patients
correlate with cellular processes?
Proteomics data
Species: human
Many genes that regulate “chemotaxis of
leukocytes” were elevated, giving
confidence that profiles generated from
both approaches can be anchored to
biological processes central to rheumatoid
arthritis.
CCL5 expression has already been implicated in rodent models of
collagen induced arthritis.
In particular, Gene View’s for
CCL4, CCL5, S100A8 and S100A9
confirmed that assays are available
for detection of human proteins
from peripheral blood samples.
IPA in Copy Number/Disease
Mechanism Research
• Goal of study: Identify genes relevant to malignancy in melanoma
samples using SNP copy number analysis
• Results: IPA analysis of Chr.3 amplified region showed multiple genes
associated with cancer and controlled by known cancer regulating genes.
Multiple molecular relationships identified between genes amplified in
Chr.3 region and genes previously associated with melanoma.
• Specific bottleneck addressed by IPA: Association found between
Chr3 genes amplified in copy number and cancer. Specifically between
MITF and melanoma.
IPA Analysis Highlights Networks of Amplified
Genes Related to Cancer
Genes amplified in Chr. 3 (outlined in
red) directly are implicated in cancerrelated processes.
They also directly regulate or are
regulate by other genes known to
impact cancer pathways (outlined in
blue).
For example:
My Pathways Identifies Regulatory Events
Connecting Sets of Genes
Chr.3 amplified genes
IPA Melanoma Genes
Genes shaded gray
are from the initial
amplification region
in Chr. 3 of
melanoma cell lines.
Genes with a white
background are
implicated in
melanoma
development, based
on evidence from the
Ingenuity Knowledge
Base.
Use the Connect
feature to see if the
Chr.3 genes are
particularly enriched
for connections to
melanoma genes.
My Pathways Reveals Strong Connections Between Genes
in Amplified Region of Chr. 3 and Melanoma-Related Genes
Connecting amplified
region genes to
melanoma implicated
genes shows a
connectivity dominated
by MITF
Many of the melanoma
genes lie outside of the
original amplified region
of Chromosome 3
identified by Affymetrix
analysis.
Understanding whether
those genes undergo
copy number changes in
the melanoma cell lines
will lend further
evidence that these
melanoma pathways are
perturbed.
IPA in Metabolic Disorders Research
•Goal of study: Analyse and compare gene expression profiles in skeletal muscle
tissue from 8 patients with morbid obesity (MO) to identify molecular mechanisms
associated to abnormalities in energy expenditure.
•Results: Perturbed energy pathways such as Cardiac ß -adrenergic signaling and
biological functions associated to dysregulated genes. Genes associated with synthesis
of protein identified in skeletal muscle tissue from morbid obesity patients
•Specific bottleneck addressed by IPA: The IPA CoreTM and Comparison analysis
identified pathways and biological functions associated to dysregulated genes in
skeletal muscle tissue from a subset of morbidly obese patients. Patients subgrouped
based on relevant biological functions and canonical pathways
Canonical Pathways across patients
Cardiac ß -adrenergic Signaling:MO4
Impaired Cardiac ß adrenergic signaling in
skeletal muscle tissue is
associated with defects in
diet-induced
thermogenesis that play
a role in the development
of morbid obesity.
Multiple Canonical
Pathways cluster across
patients 4-7
Comparison Functional Analysis groups patients
and shows role for protein biosysnthesis in obesity
Protein synthesis scores
significantly in a subset
of MO patients (MO4MO7). Protein synthesis
capabilities
arein
thus
Declines
the rate of
impaired
in
subset
ofproteins
MO
biosynthesis of
patients
that includes
in skeletal
muscle tissue
individuals
MO4-MO7.
are correlated with the
onset of insulin
resistance and obesity.
Also, biosynthesis of
protein is an important
"futile cycle" that may
function in adaptive
thermogenesis and
protection from dietinduced obesity through
the consumption of ATP.
Networks show clustering of dysregulated genes
around a single controlling node
Protein Synthesis featured
heavily for a single network
in patients 4-7
MYCN forms a common link
between most of the downregulated genes related to
the synthesis of protein
E
It seems likely that MYCN
activity is down-regulated
in skeletal muscle tissue of
patient MO4, and that
reduced activity of MYCN
protein is responsible for
the lowered expression
levels of many of the genes
related to synthesis of
protein
IPA in Metabolomics & Molecular Toxicology
Research
• Goal of study: Monitor global changes in metabolite levels in the liver
and serum of AAP treated mice to obtain insights into the disruption of
metabolic pathways related to hepatotoxicity and to identify potential
biomarkers of acute liver injury. Compare and contrast with a similar study
investigating the gene expression changes associated with AAP treated
mice.
• Results: Glutathione and Taurine Metabolic pathways implicated in cellular
response to AAP exposure at both metabolite and mRNA level. Established
toxicological pathologies associated with perturbed metabolites and genes.
• Specific bottleneck addressed by IPA: overlaying and analysis of
metabolites and genes together onto established metabolic pathways.
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28
Glutathione Metabolism in Context of Metabolite and
Transcriptome Data
Significant downregulation of
glutathione (GSH)
as well as
glutathione
disulfide (GSSG)
and glycine.
Overlay
Expression Values
from gene
expression study
of APAP treated
mice (same dose.
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29
Functional Analysis Maps Metabolite Changes to
Known APAP Induced Hepatotoxic Phenotypes
Increases and
decreases in
metabolite
levels fits well
with normal
role of
metabolites in
liver damage.
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30
Effects on Function Analysis Highlights
Potential Impact of Metabolite Changes
Understand
metabolite level
changes in the
context of their effect
on cellular,
organismal
phenotypes.
Decreased levels of
glutathione suggest
a net effect of
increased liver
damage.
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31
Networks Highlight Interplay Between Metabolites,
Genes, Pathways
Networks integrate
metabolic reactions
with signaling and
regulatory
relationships.
Dynamic nature of
networks highlights
relevance to Taurine
metabolism.
Proprietary and Confidential
32
Computational Pathways Analysis
Accelerates Biological Understanding
• Ingenuity Pathways Analysis allows scientists to
– Simultaneously analyse and compare multiple
datasets from different patient populations, different
platforms, etc.
– Gain a deeper biological understanding of the
molecular and cellular mechanisms that distinguish
one biological condition from another
– Graphically visualise biological interactions,
processes, and pathways as they change over time,
dose or disease progression
– Substantially decrease analysis time of microarray
and other high-throughput datasets
Ingenuity Systems
• Free, 2 week, fully functional trial:
• www.ingenuity.com
• Contact details:
• Adam Corner
– [email protected]
• Brian Dron
– [email protected]