Cluster analysis of ESAG and VSG gene expression. A. Signals from probes detecting VSG/VR genes. Density plot of gene-level coefficient of variation for VSG genes, defined as the standard deviation across the three biological replicates divided by the mean value of the replicates. The lines are cBF (red), slender BF (orange), stumpy BF (yellow), PF-log (dark blue), and PF-stationary (light blue). B. Heatmap of the ESAG/GRESAG and VSG/VR genes after hierarchical clustering of the individual sample log2-transformed raw expression values. The clusters were pooled into four different expression patterns as shown on left. At right the genomic location of genes is shown: 427-ES, those detected by probe-sets corresponding to sequenced 427 strain VSG expression sites; I, chromosome internal; ST, sub-telomeric as defined by occurring distal to the first or last strand-switch region on the chromosome. C. Representation of each gene class in the four clusters, classified as either sub-telomeric (VSG-ST, ESAG-ST) or chromosome internal (ESAG-I, VSG-I). Some of the genes derived from the 427 ESs last are likely not present in strain 927, while the remainder reside in regions not sequenced in strain 927 such as the intermediate or minichromosomes and the telomeres. D. Examples of VSG/VR genes from the four groups. The mean and standard deviation of the individual samples in each biological condition is shown. Genes are: group A (1, VSG Tb11.57.0024), group B (2, VSG Tb09.v4.0012, 3, VR10 Tb927.5.110, 4, VR16 Tb09.v1.0300), group C (5, unclassified VSG Tb05.5K5.440), and group D (6, atypical VSG Tb927.4.5400, 7, VR Tb927.5.291b).
Jensen et al. BMC Genomics 2009 10:482 doi:10.1186/1471-2164-10-482