Clustering of genes changing during fruit development used to normalize qRT PCR results an actin gene. a GAPDH gene and a gene of unknown function which was selected on the basis of low variability in The distribution of functional categories selleckchem for the entire array is shown in Table 2 and compared with the distribu tion of the 1955 genes selected as changing significantly during fruit development, the major clusters and the sub clusters. The distribution of MIPS functional categories changes between the whole array and the genes selected as changing during fruit development suggest that the genes selected are not a random selection from the array as a whole. For example, there appears to be a higher represen tation of genes associated with metabolism in the fruit development genes suggesting developing fruit are more active metabolically.

Interestingly, there is a slight increase in the unclassified category in the selected fruit development genes 16. 7% vs 15. 7% for the whole array, while in the ripening cluster Inhibitors,Modulators,Libraries the unclassified category Inhibitors,Modulators,Libraries is under represented compared to other clusters, which may reflect the amount of research focused on identifying and characterizing genes involved in the late stages of ripening as compared with early events in fruit development. Within the four major clusters, the genes with peak expression in mid development have a reduced represen tation of genes associated with metabolism suggesting this stage of fruit development might Inhibitors,Modulators,Libraries be less metabolically active or use fewer different metabolic genes.

In contrast, cellular transport and trans port mechanism functions are more highly represented in the mid development cluster at the time when fruit are taking up nutrients and water most rapidly. Inhibitors,Modulators,Libraries Control of cellular organization functions are represented more in the EFD and MD clusters consistent with this period being a stage of fruit development where the structure of the fruit cells is changing rapidly. In the ripening cluster there is an over Inhibitors,Modulators,Libraries representation of genes in the energy category with the lowest representation in mid develop ment. In addition the R2 sub cluster is over represented in the metabo lism category correlating with changes in energy and metabolism during late ripen ing. One feature of note was the higher proportion of genes with a cell cycle classification in the EFD cluster.

The EFD cluster contains genes for which expression peaks in the first 30 days of fruit development, the stage of development when cells are dividing. This developmental period involves the division of specific cells sellckchem to form the final apple fruit shape and since there appeared to be an increase in cell cycle associated genes during this period we identified the genes associated with the cell cycle classification for each cluster and their annotations.