Global gene expression analysis of apple fruit development from the floral bud to ripe fruit

BMC Plant Biology

Table 1 Distribution of array features

Subset/cluster^a	ESTs^b	Apple genes^c	Apple genes with hit to Arabidopsis^d	Unique Arabidopsis genes^e	Functional categories^f
whole array	15726	15145	11949	8256	63732
Selected 1986	1983	1955	1442	1330	7523
FB	315	314	225	212	1141
EFD	819	812	603	566	3042
MD	169	168	126	124	653
R	681	668	495	474	2722
EFD1	326	320	236	220	1128
EFD2	493	493	368	356	1916
R1	70	70	54	53	300
R2	195	191	154	154	885
R3	408	406	284	277	1552

The table shows the number of genes on the whole array and within the clusters as well as the number of Arabidopsis homologues and the number of MIPS function classifications identified.
a FB = full bloom; EFD = Early fruit development; MD = Mid-development; R = ripening; R1, R2, R3 = Ripening subclusters 1, 2 and 3; EFD1, EFD2 = early fruit development subclusters 1 and 2.
b The number of apple ESTs represented by the features on the array.
c The number of apple genes, tentative contigs or singletons identified by the ESTs on the array.
d Apple genes were compared with the Arabidopsis predicted protein set using BLASTx to identify similar Arabidopsis genes, the best match (with expect value better than 1 × e^-5) was used for subsequent functional analysis.
e The number of unique Arabidopsis genes identified by BLASTx using the apple genes, in many cases multiple apple genes had strongest similarity to the same Arabidopsis gene, thus fewer Arabidopsis genes were identified than apple genes.
f Functional categories found for the Arabidopsis genes were identified using the MIPS dataset funcat 1.3.

ISSN: 1471-2229