IntOGen & Gitools
integration, visualization and data-mining ofmultidimensional oncogenomic data
Christian Pérez-LlamasMaster student
Biomedical GenomicsGRIB-UPFApril 2010
Outline● Introduction● Case study● Real projects● Conclusions● Future work
Outline● Introduction● Case study● Real projects● Conclusions● Future work
Gundem et al., Nature Methods 2010
Identification of cancer related genes
identification of driver alterations
STEP 1
exp.
1
+
combination of experiments
STEP 2
exp.
2
exp.
3
exp.
n
Cance
r ty
pe A
samples
genes
not alteredaltered
genes
experiment 1
...
corrected p-value
0.05 10
International Classification of Disease from Word Health Organization
Identification of modules significantly altered in cancer
www.intogen.org
www.gitools.org
Analysis Browse ExportData
Many File Formats Supported
TSVCDMBDMGMXGMTTCM
AnalysisData Browse Export
Import data from:
● Genes significantly altered
● Modules of genes significantly altered
Data Levels Alterations
● Experiments
● Combinations
● Upregulation
● Downregulation
● Gain
● Loss
Marts
● International Cancer Genome Consorcium
AnalysisData Browse Export
AnalysisData Browse Export
AnalysisData Browse Export
AnalysisData Browse Export
Outline● Introduction● Case study● Real projects● Conclusions● Future work
Case study
● What biological processes are enriched in genes significantly up-regulated in cancer ?
● What is the correlation between different tumour types for the pattern of genes up-regulated ?
Retrieving data for the analysis
• Biological Process
Importing data from IntOGen
Importing data from IntOGen
Importing data from IntOGen
Importing data from IntOGen
Importing data from IntOGen
Importing data from IntOGen
Importing data from IntOGen
Importing data from IntOGen
Importing modules from Ensembl
Importing modules from Ensembl
Importing modules from Ensembl
Importing modules from Ensembl
Importing modules from Ensembl
Importing modules from Ensembl
Importing modules from Ensembl
Importing modules from Ensembl
Enrichment analysis
genes
mod
ule
s
Enrichmentanalysis
STEP 2
Tum
or
typ
e i
Annotated genes in module Mp-value
0.05 10
Biological modules
GO Biological processesTu
mor
type i
Transform to 1p-values < 0.05
STEP 1
Tum
or
typ
e i
... ...
...
Xi~Bin(p
i)
H0: p
m = p
i
H1: p
m > p
i
gen
es
Enrichment analysis
Enrichment analysis
Enrichment analysis
Enrichment analysis
Enrichment analysis
Enrichment analysis
Enrichment analysis
Enrichment analysis
Correlations
Correlations
Correlations
Correlations
Correlations
Outline● Introduction● Case study● Real projects● Conclusions● Future work
Real projects● RBP2 function
● Functional protein divergence
● Study of altered regulatory programs in cancer
● Stress response genes and transition into increased malignant states
● Comparison of alteration patterns among tumor types
Functional Enrichment of RBP2 targets at different time points of differentiation
Lopez-Bigas et al., Molecular Cell 2008
RBP2
● RBP2 function
● Functional protein divergence
● Study of altered regulatory programs in cancer
● Stress response genes and transition into increased malignant states
● Comparison of alteration patterns among tumor types
Real projects
Lopez-Bigas et al., Genome Biology 2008
Outline● Introduction● Case study● Real projects● Conclusions● Future work
Conclusions● IntOGen is a novel framework for Oncogenomics data
integration
● IntOGen.org is a discovery tool for cancer researchers
● Gitools main features are:
● Interactive heatmap● Import from Biomart● Import from IntOGen● Command line option
Future work● Biomart compatible interface for IntOGen● Implement more analysis:
● GSEA● Clustering● Modules hierarchy aware enrichment like Gostats● Connection with R
● Implement more editors:● Table and modules editor
AcknowledgementsNuria López-Bigas
Gunes Gundem
Jordi Deu-Pons
Khademul Islam
Michael Schroeder
Alba Jené-Sanz
Xavier Rafael
Remember to visitwww.intogen.orgwww.gitools.org
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