1. Mining publicly available microarray data Frances Turner Fsturner@ic.ac.uk

2. Introduction Publicly available data Method for data mining Application to Tuberculosis and Campylobacter

3. Capsule synthesis in C.jejuni In which dataset(s) do these genes show changed expression? Identify useful data Improve biological understanding

4. Publicly available data Increasing volume of data Different depositories Different standards Difficult to compare experiments

5. Publicly available data Campylobacter 18 experiments 126 conditions M.bovis/M.tuberculosis 34 experiments 539 conditions

6. Identification of sets of differentially expressed genes GSEA commonly used (Subramanian et al 2005) Threshold independent Small but biologically significant changes

7. GSEA applied to multiple expression datasets Cj1099 Cj0812 Cj1494 c Cj1457 c Cj0434 Cj1307 Cj0028 Cj1294 Cj1393 Cj1303 Cj1368 Cj0597 Cj1309 c Cj0505 c

8. GSEA applied to multiple expression datasets Cj1099 Cj0812 Cj1494 c Cj1457 c Cj0434 Cj1307 Cj0028 Cj1294 Cj1393 Cj1303 Cj1368 Cj0597 Cj1309 c Cj0505 c Cj0172 Cj1099 Cj0028 Cj0812 Cj1494 c Cj0741 Cj1457 c Cj1303 Cj0434 Cj1393 Cj1307 Cj1294 Cj1393 Cj1309 c Cj0812 Cj1494 c Cj1307 Cj0434 Cj1393 Cj0028 Cj1294 Cj0597 Cj0145 c Cj1368 Cj0432 Cj1309 c Cj0505 c

9. GSEA applied to multiple expression datasets Allows correction for multiple datasets Not confounded by correlations between datasets

10. Capsule synthesis in C.jejuni ConditionData setDirection of change p-value Anaerobic v control E-BUGS-19Down3.75 e-06 Microaerobic v control E-BUGS-19Down2.88 e-05 dksA mutant v wild type GSE9866Down2.55 e-07 Invivo v chemostat GSE9942Down2.63 e-09 CmeR mutant v wild type GSE5421Both7.21 e-09

11. Nitrogen metabolism in M.bovis ConditionData setDirection of change p-value Anaerobic M.bovis v control M.tuberculosis GSE11315Down0.001 M.bovis v control M.tuberculosis GSE11315Down0.002 M.tuberculosis 4mM H2O2 v M.tuberculosis control GSE365Down0.002 Mpr mutant v controlGSE6750Up0.003 espR mutant v controlGSE12379Down0.007

12. Collect available microarray data Put different datasets in to comparable formats GSEA based analysis Identification of experimental conditions of interest Summary

13. 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.