Download - IntOGen & Gitools
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IntOGen & Gitools
integration, visualization and data-mining ofmultidimensional oncogenomic data
Christian Pérez-LlamasMaster student
Biomedical GenomicsGRIB-UPFApril 2010
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Outline● Introduction● Case study● Real projects● Conclusions● Future work
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Outline● Introduction● Case study● Real projects● Conclusions● Future work
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Gundem et al., Nature Methods 2010
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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
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Identification of modules significantly altered in cancer
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www.intogen.org
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www.gitools.org
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Analysis Browse ExportData
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Many File Formats Supported
TSVCDMBDMGMXGMTTCM
AnalysisData Browse Export
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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
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AnalysisData Browse Export
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AnalysisData Browse Export
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AnalysisData Browse Export
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Outline● Introduction● Case study● Real projects● Conclusions● Future work
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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 ?
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Retrieving data for the analysis
• Biological Process
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Importing data from IntOGen
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Importing data from IntOGen
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Importing data from IntOGen
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Importing data from IntOGen
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Importing data from IntOGen
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Importing data from IntOGen
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Importing data from IntOGen
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Importing data from IntOGen
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Importing modules from Ensembl
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Importing modules from Ensembl
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Importing modules from Ensembl
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Importing modules from Ensembl
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Importing modules from Ensembl
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Importing modules from Ensembl
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Importing modules from Ensembl
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Importing modules from Ensembl
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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
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Enrichment analysis
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Enrichment analysis
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Enrichment analysis
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Enrichment analysis
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Enrichment analysis
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Enrichment analysis
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Enrichment analysis
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Enrichment analysis
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Correlations
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Correlations
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Correlations
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Correlations
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Correlations
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Outline● Introduction● Case study● Real projects● Conclusions● Future work
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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
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● 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
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Outline● Introduction● Case study● Real projects● Conclusions● Future work
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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
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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
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AcknowledgementsNuria López-Bigas
Gunes Gundem
Jordi Deu-Pons
Khademul Islam
Michael Schroeder
Alba Jené-Sanz
Xavier Rafael
Remember to visitwww.intogen.orgwww.gitools.org