Table 1.

Expressed sequence tags (ESTs) significantly up- or down-regulated in the shoot apical meristem (SAM)

	Three microarrays combineda	Apex ESTsb	2-week-shoot ESTsb
No. of spots	37 660	10 816	1781
Up-regulated in the SAM	2783 (7.4)	894c (8.3)	138 (7.7)
Down-regulated in the SAM	2248 (6.0)	231 (2.1)	551 (31)

Numbers of ESTs significantly (P<0.0001) up- or down-regulated in the SAM relative to the seedling are presented. Parentheses indicate percentages of significant ESTs relative to total number of maize ESTs in each category.

^aUnique genes among these 37 660 spots were estimated to be 21 721. To estimate this, maize EST contigs (MECs with a 95% cut-off as of March 2006; Fu et al., 2005) that contain EST sequences on the three microarrays were searched. Then maize genomic loci that match these MECs plus EST singletons were searched for within a partial genome assembly of the maize inbred line B73 (MAGI3.1; http://magi.plantgenomics.iastate.edu) that has been estimated to tag between 75% and 90% of the maize gene space (Fu et al., 2005). These genomic loci were considered to be unique genes. If no genomic loci were found, MECs and EST singletons were considered to be unique genes. If only ‘unique genes’ are considered, 2292 and 1791 genes were up- and down-regulated genes, respectively.

^bApex ESTs (Table S1) and 2-week-shoot ESTs (library 947, 2-week-shoots; Table S5) represent only a portion of the ESTs on the three microarrays.

^cOut of the 894 up-regulated Apex ESTs, 312 were ‘Apex-unique’ (Table S1).