Screening significantly hypermethylated genes in fetal tissues compared with maternal blood using a methylated-CpG island recovery assay-based microarray

Table 2 Top 15 hypermethylated genes identified using the MIRA-based microarray

Gene	Changed probes	Average ratio^a	Position^b	Gene description	Phenotype MIM Accession No.^c
PITX2	27	3.19	I and D	Paired-like homeodomain 2	180500, 137600, 604229, 180550
PAX6	20	2.34	P and I	Paired box 6	106210, 604219, 120430, 120200, 136520, 206700, 148190, 165550, 604229
NR2F2	17	3.22	P, I and D	Nuclear receptor subfamily 2, group F, member 2
MNX1	15	2.50	P, I and D	Motor neuron and pancreas homeobox 1	176450
TLX3	15	3.69	P and D	T-cell leukemia homeobox 3
PAX9	15	2.33	P and I	Paired box 9	604625
SALL1	15	2.27	P, I and D	Sal-like 1 (Drosophila)	107480
MAD1L1	14	3.18	I	MAD1 mitotic arrest deficient-like 1 (yeast)	176807
TBX3	14	4.50	P, I and D	T-box 3	181450
HLX	14	2.01	P, I and D	H2.0-like homeobox
PDX1	13	2.88	P, I and D	Pancreatic and duodenal homeobox 1	606392, 260370, 125853
TFAP2C	13	4.78	P	Transcription factor AP-2 gamma
SIX1	12	3.13	P, I and D	SIX homeobox 1	608389, 605192
SIM1	12	2.98	P and I	Single-minded homolog 1 (Drosophila)	601665
OTX2	12	3.39	P and D	Orthodenticle homeobox 2	610125, 613986

Several probes for each gene are present on the microarray. ^aThe average ratio of the probe density of the positive probe in placental tissue to that in the maternal peripheral blood calculated using the SAM software. ^bThe letters in this column refer to different regions of the gene: P, promoter; I, inside; D, downstream. ^cThe phenotype MIM Accession Number is from the OMIM database (http://www.ncbi.nlm.nih.gov/omim).