Navigating gene networksby text mining and statistical analysis

Simon Vanden Bussche .:.:. Leon-Charles Tranchevent .:.:. Shi Yuhttp://homes.esat.kuleuven.be/~vandenbs/

Text mining

Text miningsearching for genes in the PubMeb database

Text mining

• Java

searching for genes in the PubMeb database

Text mining

• Java

• Apache Lucene

searching for genes in the PubMeb database

Text mining

• Java

• Apache Lucene

• MySQL

searching for genes in the PubMeb database

Text mining

• Java

• Apache Lucene

• MySQL

• Matlab

searching for genes in the PubMeb database

Text mining

• Java

• Apache Lucene

• MySQL

• Matlab

• BioLayout

searching for genes in the PubMeb database

Text mining

Text miningno treshold

Text miningno treshold treshold: 2

Text mining

First version

no treshold treshold: 2

Text mining

Case sensitive version

no treshold treshold: 2

Statistical analysis

Statistical analysisknown disease genes vs. regular genes

Statistical analysis

• ENSEMBL

• ASTD

known disease genes vs. regular genes

Statistical analysis

• ENSEMBL

• ASTD

• OMIM

• GAD

known disease genes vs. regular genes

Statistical analysis

Statistical analysis• What is compared?

Statistical analysis• What is compared?

Statistical analysis

• Matlab programming

• What is compared?

Combined results

Combined results

Combined results

• Text mining result

Combined results

• Text mining result

• Different tresholds

Combined results

• Text mining result

• Different tresholds

• Number of first neighbours

• Number of disease neighbours

Combined results

• Text mining result

• Different tresholds

• Number of first neighbours

Combined results

• Text mining result

• Different tresholds

• Number of first neighbours

• Number of disease neighbours

d

Combined results

Combined resultsScatter plots

Combined resultsScatter plots

number of neighbours versus percentage of disease neighbours

num

ber

of n

eigh

bour

s

percentage of disease neighbours

Combined results

Combined resultsGeneral comparison

Homology

Combined resultsGeneral comparison

Homology

• extra boxplot for neighbours of disease genes

Combined resultsGeneral comparison

Homology

• extra boxplot for neighbours of disease genes• doing the same comparisons

http://homes.esat.kuleuven.be/~vandenbs/

http://homes.esat.kuleuven.be/~vandenbs/

Questions?