Ferreira et al. BMC Genomics 2010, 11:93 http://www.biomedcentral.com/1471-2164/11/93 Page 11 of 17 Figure 9 Schematic scheme illustrating how tuber volume is measured using X-ray CT. Potato plants are scanned with X-ray in a chamber containing an X-ray beam and a two dimensional detector. After projecting X-ray images of the potato plant on the detector at different angles, the projections are reconstructed in silico to create a three dimensional image. From this image the tuber volume can be calculated. a stolon/swollen stolon, diurnally in leaves and between growing/non-growing tubers were selected. To further decrease the number of features, only those features dif- ferentially expressed under all conditions were selected which reduced the number to 1662 (Figure 13A). K- means clustering analysis was performed on these fea- tures and most starch biosynthetic genes were present in three clusters. These clusters also showed the expected expression patterns for starch biosynthetic genes (Figure 13B). A functional assignment on the 913 features present in these three clusters was performed which showed that 37% of the features were involved in metabolism and a further 9% storage protein related (Figure 13C). Transcription factors made up 6% of the features and these were further investigated. Arabidopsis orthologs for these transcription factors were identified and used to gather more information on their possible function. Six of these transcription factors showed increased expression in Arabidopsis suspension culture fed with sucrose [50] and most of these genes were also down-regulated in leaves when the dark per- iod was extended [51]. Figure 14 contain the expression profiles of these transcription factors including the iden- tifiers of their orthologs in Arabidopsis. All of these transcription factors, with the exception of AT4G00870 and AT4G32730, were also down-regulated in the 35S:: Figure 10 Potato tuber segmentation and volume calculation. A) Two dimensional X-ray images illustrating that potato tubers can be distinguished from the surrounding soil. The histogram shows that segmentation is possible. The red bar indicates the grey level threshold selected. B) Linear regression of X-ray calculated and real volume measurements confirming the accuracy of X-ray CT calculated volumes.