Table 3.

Case studies using the Maize Microarray Annotation Database

Reference	Description *	Table (see Reference)	Total	Genomic Annotation Groups#
				GMS	GMA	G	E	AM	I
Ma et al. [4]	a	Table S3	2285	1614 (70.6%)	141 (6.2%)	54 (2.4%)	108 (4.7%)	148 (6.5%)	220 (9.6%)
Ma et al. [4]	b	Table S4	281	209 (74.4%)	11 (3.9%)	7 (2.5%)	13 (4.6%)	27 (9.6%)	14 (5.0%)
Casati et al. [30]	c	Table S1	2092	1373 (65.6%)	142 (6.8%)	58 (2.8%)	111 (5.3%)	134 (6.4%)	274 (13.1%)
Skibbe et al. [31]	d	Table S1	449	329 (73.3%)	6 (1.3%)	18 (4.0%)	16 (3.6%)	35 (7.8%)	45 (10.0%)
Skibbe et al. [31]	e	Table S1	399	279 (69.9%)	15 (3.8%)	16 (4.0%)	18 (4.5%)	23 (5.8%)	48 (12.0%)
Wang et al. [4]	f	Table S3	416	159 (38.2%)	58 (13.9%)	22 (5.3%)	57 (13.7%)	14 (3.4%)	106 (25.5%)
Rajhi et al. [32]	g	Table S2	239	177 (74.1%)	15 (6.3%)	5 (2.1%)	10 (4.2%)	12 (5.0%)	20 (8.4%)
Rajhi et al. [32]	h	Table S3	336	278 (82.7%)	7 (2.1%)	8 (2.4%)	14 (4.2%)	15 (4.5%)	14 (4.2%)

* Description

a = Transcripts differentially expressed between meiotic and post-meiotic stages

b = Zinc finger-related proteins

c = Transcripts that are expressed differentially between mbd101 and chc101 RNAi transgenic plants and WT non transgenic siblings under control and/or UV-B conditions.

d = Up-regulated genes between Mu-active vs inactive lines (Mitotic stage)

e = Down-regulated genes between Mu-active vs inactive lines (Mitotic stage)

f = 1.0 mm stage-specific genes of ms8 anthers expressed at later stages in normal anthers

g = Genes up-regulated in maize root cortex during aerenchyma formation

h = Genes down-regulated in maize root cortex during aerenchyma formation

^# Genomic annotations:

GMS = Annotation by sense gene model

GMA = Annotation by antisense gene model

G = Annotation by gDNA (Genomic position)

E = Annotation by EST

AM = Ambiguous annotation

I = Inconclusive annotation