Ferreira et al. BMC Genomics 2010, 11:93 http://www.biomedcentral.com/1471-2164/11/93 Page 13 of 17 Figure 13 Comparative analysis of transcription profiles. A) Venn diagramm showing 1662 features differentially expressed under all conditions selected B) K means clustering showing 5 clusters (A-E) with three clusters having the desired pattern of expression for starch biosynthetic genes (B-D). C) Functional assignment of features present in clusters B-D). determined in a natural environment. Tuber growth velocity could not be correlated to starch biosynthetic gene expression, although it was clear that gene expres- sion is different between growing and non-growing tubers. The relationship between gene expression and growth velocity seems to be qualitative rather than quantitative and the data provides important informa- tion towards the identification of factors determining potato tuber growth. Comparative analysis made it possible to select for genes differentially regulated under various conditions. Since the microarray experiments performed were set up to comprise conditions of active starch biosynthesis, it was believed that comparative analysis of transcription profiles would select for genes involved in this process. Cluster analysis of differentially expressed genes revealed clusters containing genes known to be involved in starch biosynthesis, and further analysis revealed transcription factors which could be used to influence starch bio- synthesis. Closer analysis reveal that orthologs of these transcription factors in Arabidopsis are positively regu- lated by sucrose indicating that they could be interesting targets for influencing starch biosynthesis. Methods Plants and growth conditions Solanum tuberosum (cv Solara) were propagated in tis- sue culture on MS medium [53] containing 2% sucrose. To obtain tubers, plants were transferred to soil and cultivated until harvest in individual pots in the green- house or growth chambers. For transcriptional analysis of potato leaves over a diurnal period, plants were grown in a growth chamber under a 14 hour light and 10 hour dark cycle. Plants for the tuber induction and X-ray CT studies were grown in the greenhouse under normal long day conditions. Plants used for analysing for the diurnal rhythm in tuber gene expression were grown in growth chambers under normal long day conditions. RNA isolation, cRNA synthesis and Cy3-labeling Isolation of total RNA was performed as described pre- viously [54]. POCI array and database The construction of the POCI array and database has been described in detail [29]. Sample preparation and microarray hybridization For each hybridisation at least two biological replicates were included. For diurnal leaf time-points five different leaves from five plants were sampled for each biological replicate. For tuber induction samples stolon or tuber material from 40 plants were pooled into two groups according to the developmental stages. For the hybridi- zation comparing fast and slow growing tubers, two independent samples were taken from each tuber and treated as biological replicates. RNA purity was mea- sured by the ND-1000 Spectrophotometer (NanoDrop