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We applied the statistical method proposed by us for a GO based microarray data interpretation and the commonly used threshold-based (hypergeometric and Fisher's exact) and threshold independent method methods (Kolmogorov-Smirnov test and Student's t-test) in a comparative case study to two bacterial microarray data sets:
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influence of oxygen availabilty on E.coli (strain K12)
download data as probabilities of differential expression
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knockout of the gene for the transcription factor Lrp in E.coli (strain K12)
download data as expression ratios
download data as ppde
1) For the growth under anaerobic conditions a priori down-regulation of the main cellular functions involved in aerobic energy production is expected. The results from our analysis clearly meet this expectation since for example the GO nodes "proton-transporting ATP synthase complex" and "oxidative phosphorylation" were identified as significantly altered in their expression profile.
2) For the lrp knockout central energy consuming biosynthetic pathways of, for example, "protein biosynthesis" and "amino acid biosynthesis" were identified as affected by our tool. In addition, GO nodes that represent transport processes and catabolic pathways were found. The results fit to the biological expectation standing behind this experiment since Lrp is a global transcriptional regulator which activates genes involved in amino acid metabolism and it regulates the transport of smaller molecules.
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Supplementary material: |
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Supplementing the above mentioned experiment of a Kang et al. (2005) who investigated the switch from aerobic to anaerobic life conditions in E. coli another expression data set from Salmon et al. (2005) is available that reflects the effect of an Anr knockout. Anr is a global transcriptional regulator which regulates the expression of genes in response to changes in oxygen tension in E. coli. Thus, it is one of the main transcriptional regulator that is responsible for the changes in gene expression after switching to anaerobic life conditions. Therefore an overlapping set of genes is expected to be differentially epxressed when comparing wild type cells grown under aerobic and anaerobic conditions with wild type cells and Anr knockout cells, both grown under anaerobic conditions. The corresponding data set of the latter experiment can be downloaded here (as probabilities of differential expression): Anr knockout microarray data subset from Salmon et al. 2005
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