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Introduction
• Publicly available data
• Method for data mining
• Application to Tuberculosis and Campylobacter
Capsule synthesis in C.jejuni
• In which dataset(s) do these genes show changed expression?
• Identify useful data
• Improve biological understanding
Publicly available data
• Increasing volume of data
• Different depositories
• Different standards
• Difficult to compare experiments
Publicly available data
Campylobacter
18 experiments126 conditions
M.bovis/M.tuberculosis
34 experiments539 conditions
Identification of sets of differentially expressed genes
• GSEA commonly used (Subramanian et al 2005)
• Threshold independent
• Small but biologically significant
changes
GSEA applied to multiple expression datasets
Cj1099Cj0812Cj1494cCj1457cCj0434Cj1307Cj0028Cj1294Cj1393Cj1303Cj1368Cj0597Cj1309cCj0505c
GSEA applied to multiple expression datasets
Cj1099Cj0812Cj1494cCj1457cCj0434Cj1307Cj0028Cj1294Cj1393Cj1303Cj1368Cj0597Cj1309cCj0505c
Cj0172Cj1099Cj0028Cj0812Cj1494cCj0741Cj1457cCj1303Cj0434Cj1393Cj1307Cj1294Cj1393Cj1309c
Cj0812Cj1494cCj1307Cj0434Cj1393Cj0028Cj1294Cj0597Cj0145cCj1368Cj0432Cj1309cCj0505c
GSEA applied to multiple expression datasets
• Allows correction for multiple datasets
• Not confounded by correlations between datasets
Capsule synthesis in C.jejuni
Condition Data set Direction of change
p-value
Anaerobic v control
E-BUGS-19 Down 3.75 e-06
Microaerobic v control
E-BUGS-19 Down 2.88 e-05
dksA mutant v wild type
GSE9866 Down 2.55 e-07
Invivo v chemostat
GSE9942 Down 2.63 e-09
CmeR mutant v wild type
GSE5421 Both 7.21 e-09
Nitrogen metabolism in M.bovis
Condition Data set Direction of change
p-value
Anaerobic M.bovis v control M.tuberculosis
GSE11315 Down 0.001
M.bovis v control M.tuberculosis
GSE11315 Down 0.002
M.tuberculosis 4mM H2O2 v M.tuberculosis control
GSE365 Down 0.002
Mpr mutant v control GSE6750 Up 0.003
espR mutant v control GSE12379 Down 0.007
Collect available microarray data
Put different datasets in to comparable formats
GSEA based analysis
Identification of experimental conditions of interest
Summary
Work in progress
• Collaboration with Chris Tomlison to
create user interface
• Host of CISBIC server
• Allow users to test their own gene
sets or expression datasets.
