BMC Genomics 2008, 9:298 http://www.biomedcentral.com/1471-2164/9/298 A e c n e c s e r o u l f 5 y C 100000 10000 1000 100 10 1 1 B 10 100 1000 10000 100000 Cy3 fluorescence Highly increased in BSF Increased in BSF Not significantly increased in BSF Not significantly increased in PCF Increased in PCF Highly increased in PCF -2.4 0 2.4 FOivgeurrveiew1 of developmental transcriptome changes in the membrane trafficking system of trypanosomes Overview of developmental transcriptome changes in the membrane trafficking system of trypanosomes. Panel A: Scatter plot of raw data for all 3600 spots on a representative microarray used for developmental expression experiments. Cy5 fluorescence is plotted on the Y-axis (bloodstream, BSF) and Cy3 fluorescence on the X-axis (procyclic, PCF). Spots with a BSF/PCF ratio above two are highlighted in red, while spots with a PCF/BSF ratio above two are highlighted in green. Panel B: Clustering of the data for eight microarray experiments comparing BSF to PCF, representing four biological replicates plus relevant dye-swaps. The scale indicates the colour scheme for the z-score of the data, i.e. how far and in what direction, the ratio for each spot deviates from the mean for each array, expressed in units of standard deviation; bright red indicates significant upregulation in BSF, bright green indicates significant upregulation in PCF, dark colours or black indicate no differential expression between the two developmental stages. For each target gene, the four replicate spots on the array were averaged. White indicates data points rejected because of too much variability in the replicate spots. A small but sig- nificant number of ORFs exhibit strong developmental regulation. Page 4 of 28 (page number not for citation purposes)