navigating gene networks
TRANSCRIPT
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Navigating gene networksby text mining and statistical analysis
Simon Vanden Bussche .:.:. Leon-Charles Tranchevent .:.:. Shi Yuhttp://homes.esat.kuleuven.be/~vandenbs/
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Text mining
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Text miningsearching for genes in the PubMeb database
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Text mining
• Java
searching for genes in the PubMeb database
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Text mining
• Java
• Apache Lucene
searching for genes in the PubMeb database
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Text mining
• Java
• Apache Lucene
• MySQL
searching for genes in the PubMeb database
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Text mining
• Java
• Apache Lucene
• MySQL
• Matlab
searching for genes in the PubMeb database
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Text mining
• Java
• Apache Lucene
• MySQL
• Matlab
• BioLayout
searching for genes in the PubMeb database
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Text mining
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Text miningno treshold
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Text miningno treshold treshold: 2
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Text mining
First version
no treshold treshold: 2
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Text mining
Case sensitive version
no treshold treshold: 2
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Statistical analysis
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Statistical analysisknown disease genes vs. regular genes
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Statistical analysis
• ENSEMBL
• ASTD
known disease genes vs. regular genes
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Statistical analysis
• ENSEMBL
• ASTD
• OMIM
• GAD
known disease genes vs. regular genes
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Statistical analysis
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Statistical analysis• What is compared?
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Statistical analysis• What is compared?
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Statistical analysis
• Matlab programming
• What is compared?
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Combined results
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Combined results
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Combined results
• Text mining result
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Combined results
• Text mining result
• Different tresholds
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Combined results
• Text mining result
• Different tresholds
• Number of first neighbours
• Number of disease neighbours
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Combined results
• Text mining result
• Different tresholds
• Number of first neighbours
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Combined results
• Text mining result
• Different tresholds
• Number of first neighbours
• Number of disease neighbours
d
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Combined results
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Combined resultsScatter plots
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Combined resultsScatter plots
number of neighbours versus percentage of disease neighbours
num
ber
of n
eigh
bour
s
percentage of disease neighbours
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Combined results
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Combined resultsGeneral comparison
Homology
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Combined resultsGeneral comparison
Homology
• extra boxplot for neighbours of disease genes
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Combined resultsGeneral comparison
Homology
• extra boxplot for neighbours of disease genes• doing the same comparisons
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http://homes.esat.kuleuven.be/~vandenbs/
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http://homes.esat.kuleuven.be/~vandenbs/
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Questions?