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LearningObjectivesofModule
• Beabletoperformpathwayandnetwork-baseddataanalysisusingReactomeFIViz app
Reactome Functional Interaction (FI) Network and ReactomeFIViz app
• No single mutated gene is necessary and sufficient to cause cancer.
• Typically one or two common mutations (e.g. TP53) plus rare mutations.
• Analyzing mutated genes in a network context:
• reveals relationships among these genes.
• can elucidate mechanism of action of drivers.
• facilitates hypothesis generation on roles of these genes in disease phenotype.
• Network analysis reduces hundreds of mutated genes to < dozen mutated pathways.
What is a Functional Interaction?
Input1-Input2, Input1-Catalyst,Input1-Activator, Input1-
Inhibitor, Input2-Catalyst, Input2-Activator, Input2-Inhibtior,
Catalyst-Activator, Catalyst-Inhibitor, Activator-Inhibitor
Reaction Functional Interactions
• Convert reactions in pathways into pair-wise relationships
• Functional Interaction: an interaction in which two proteins are involved in the same reaction as input, catalyst, activator and/or inhibitor, or as components in a complex
Method and practical application: A human functional protein interaction network and its application to cancer data analysis, Wu et al. 2010 Genome Biology.
ConstructionoftheFINetwork
ReactomeKEGG
Encode TF/TargetTRED TF/Target
NCI-BioCartaNCI-Nature
Data sources for annotated FIs
Naïve Bayes Classifier
Trained by Validated by
Predicted FIs Annotated FIs
FI Network
Human PPI
Fly PPI
Domain InteractionPrieto’s Gene ExpressionLee’s Gene Expression
GO BP Sharing
Yeast PPIWorm PPI
Data sources for predicted FIs
Mouse PPI
Panther Pathways
Featured by
Extracted fromPredicted by
328K interactions 12K proteins
Projecting Experimental Data onto FI Network
127CancerDriverGenes
ACVR1B, ACVR2A, AJUBA, AKT1, APC, AR, ARHGAP35, ARID1A, ARID5B, ASXL1, ATM, ATR, ATRX, AXIN2, B4GALT3, BAP1, BRAF, BRCA1, BRCA2, CBFB, CCND1, CDH1, CDK12, CDKN1A, CDKN1B, CDKN2A, CDKN2C, CEBPA, CHEK2, CRIPAK, CTCF, CTNNB1, DNMT3A, EGFR, EGR3, EIF4A2, ELF3, EP300, EPHA3, EPHB6, EPPK1, ERBB4, ERCC2, EZH2, FBXW7, FGFR2, FGFR3, FLT3, FOXA1, FOXA2, GATA3, H3F3C, HGF, HIST1H1C, HIST1H2BD, IDH1, IDH2, KDM5C, KDM6A, KEAP1, KIT, KRAS, LIFR, LRRK2, MALAT1, MAP2K4, MAP3K1, MAPK8IP1, MECOM, MIR142, MLL2, MLL3, MLL4, MTOR, NAV3, NCOR1, NF1, NFE2L2, NFE2L3, NOTCH1, NPM1, NRAS, NSD1, PBRM1, PCBP1, PDGFRA, PHF6, PIK3CA, PIK3CG, PIK3R1, POLQ, PPP2R1A, PRX, PTEN, PTPN11, RAD21, RB1, RPL22, RPL5, RUNX1, SETBP1, SETD2, SF3B1, SIN3A, SMAD2, SMAD4, SMC1A, SMC3, SOX17, SOX9, SPOP, STAG2, STK11, TAF1, TBL1XR1, TBX3, TET2, TGFBR2, TLR4, TP53, TSHZ2, TSHZ3, U2AF1, USP9X, VEZF1, VHL, WT1
AR
RPL22
NPM1
RPL5
TAF1
CEBPA
RB1CCND1
ERCC2
BRCA2
ATR
EZH2
ASXL1
CHEK2
BAP1
TET2
SIN3A
GATA3
FBXW7
EPHB6
KDM5C
NSD1
HIST1H1C
USP9X
RAD21
BRCA1
KDM6A SMC3
AJUBA
FOXA1
FOXA2
PCBP1
U2AF1
ATM
DNMT3A
STAG2ATRX
CTCF
SMC1A
ELF3
NFE2L2
SF3B1
KEAP1
TP53
WT1
CDKN1B
CDKN2C
CDKN2A
CDKN1A
KIT
FGFR3MAP2K4
PDGFRA
NRAS
BRAF
KRAS
LIFR
PIK3CG
TLR4
MAP3K1
PTPN11
CDH1
FLT3
AKT1
HGF
ARHGAP35
FGFR2
MTORPIK3CA
EGFR
PIK3R1
PPP2R1AERBB4
NF1
PTEN CTNNB1
SOX9
EPHA3
EP300
NOTCH1
ARID5B
NCOR1
HIST1H2BDARID1A
SMAD4
SMAD2
TBL1XR1
CBFB
AXIN2
EIF4A2
RUNX1
APC
STK11
ACVR2A
TGFBR2LRRK2
ACVR1B
MECOM
SOX17
Signaling by EGFR, FGFR, SCF-KIT, etc.
Cell CycleTP53 Pathway
Signaling by Notch, Wnt, TGF-beta, SMAD2/3, etc.
Module-Based Prognostic Biomarker in ER+ Breast Cancer
Cell Cycle M Phase
Aurora B Signaling
Low expression
High expression
Measure levels of expression of the genes in this network
moduleGuanming Wu
Visualize Cancer Targetome in the Reactome FI Network
TCGA GBM Mutation Profile
3) Pathway-Based Modeling
• Apply list of altered {genes, proteins, RNAs} to biological pathways.
• Preserve detailed biological relationships.
• Attempt to integrate multiple molecular alterations together to yield lists of altered pathway activities.
• Pathway modeling shades into Systems Biology
Types of Pathway-Based Modeling
• Partial differential equations/boolean models, e.g. CellNetAnalyzer
• Mostly suited for biochemical systems (metabolomics)
• Network flow models, e.g. NetPhorest, NetworKIN
• Mostly suited for kinase cascades (phosphorylation info)
• Transcriptional regulatory network-based reconstruction methods, e.g. ARACNe (expression arrays)
• Probabilistic graph models (PGMs), e.g. PARADIGM
• Most general form of pathway modeling for cancer analysis at this time.
Probabilistic Graphical Model (PGM) based Pathway Analysis
• Attempt to integrate multiple molecular alterations together to yield lists of altered pathway activities.
• Many omics data types available for one single patient
• CNV, gene expression, methylation, somatic mutations, etc.
• Pathway and network-based Simulation
• Find significantly impacted pathways for diseases
• Link pathway activities to patient phenotypes
• Predict drug effects: one drug or multiple drugs together?
PARADIGM
MDM2
TP53
Apoptosis
Mutation
mRNA Change
CNV
Mass spec
Apoptosis
MDM2gene
MDM2RNA
MDM2protein
TP53gene
TP53RNA
TP53protein
MDM2Active protein
TP53Active protein
w1
w2
w3
w4
w5
w6w7
Adapted from Vaske, Benz et al. Bioinformatics 26:i237 (2010)
Probabilistic Graphical Models (PGMs) for Reactome Pathways
1
2
PGM-basedSinglePatientPathwayView
Building Quantitative Models for ReactomePathways
ReactomePathwayODE Model
Probabilistic Graphical Model
Boolean Network Model
Future Direction
Tutorial
MajorFeaturesinReactomeFIViz
A1) Reactome Pathway Enrichment Analysis
Displaying Reactome Pathways in the FI Network View
Pathway Enrichment Analysis
Visualize Cancer Targetome in Reactome Pathways
A2) De Novo Subnetwork Construction & Clustering
Extract and Cluster, and Annotate Altered
GenesDisease “modules” (10-30)
CuratedPathway DBs
UncuratedInteractionEvidence
+Reactome Functional Interaction Network
(~12K proteins; ~328K interactions)
Machine Learning
Cytoscape using ReactomeFIViz app
Project your data into Reactome FI
Network
+
Uploadyourdata
• FI plug-in supports four file formats:• Simple gene set: one line per gene• Gene/sample number pair. Contains two required columns, gene and
number of samples having gene mutated, and an optional third column listing sample names (delimited by semi-colon ;)
• NCI MAF (mutation annotation file)• Sample Gene Expression data file
FileFormats• Choose Plugins, Reactome FIs.
• FI plug-in supports four file formats:
• Gene list
• Gene-Sample gene
• NCI Mutation Annotation File
• Microarray Expression Data
GeneSet-basedAnalysis
FIResultsDisplay
• Constructed network is displayed in the Network View panel using an FI specific visual style
The main features ofthe plug-in are invokedfrom a popup menu,which can be displayedby right clicking a whitespace, a node or edgein the the network viewpanel.
FIAnnotations
• Provides detailed information on selected FIs.
• Three edge attributes are created: • FI Annotation.
• FI Direction.
• FI Score (for predicted FI).
• Edges display direction attribute values. • --> for activating/catalyzing.
• --| for inhibition.
• solid line for complexes or inputs.
• --- for predicted FIs.
The main features of the plug-in are invoked from a popup menu, which can be displayed by right clicking a node or edge in the the network view panel.
Query FI Source
Annotated FIs Predicted FIs
• Runs spectral partition based network clustering (Newman, 2006) on the displayed FI network.
• Nodes in different network modules will be shown in different colours (max 15 colours).
• Analyze cancer mutation data with HotNet algorithm (Vandin, 2012)
Cluster FI Network
• Pathway or GO term enrichment analysis on individual network modules. • Use filter to remove small network modules
• Filter by FDR
Analyze ModuleFunctions
• Select a pathway in "Pathways in Network/Modules" tabs, right click, select "Show Pathway Diagram”
Other Features – Show Pathway Diagrams
• View detailed annotations for the selected gene or protein.
• Annotations are sortable by PubMed ID, Cancer type, status, and other criteria.
Other Features – NCI Cancer Gene Index
• Load the NCI disease terms hierarchy in the left panel.
• Select a disease term in the tree to select all nodes that have this annotation or one of its sub-terms.
Other Features – Overlay Cancer Gene Index
• View detailed variant annotations for the selected gene or protein from COSMIC database.
Other Features – COSMIC
ModuleBasedSurvivalAnalysis
• Discover Prognostic Signatures in Disease Module Datasets.
• Based on a server-side R script that runs either CoxPH or Kaplan-Meyer survival analysis.
• Requires appropriate clinical data file.
For any questions or feedback, please contact [email protected]