A common gene expression signature in Huntington’s disease patient brain regions

BMC Medical Genomics

Table 5 Microarray datasets used in this study

Set	Accession	ctr/patient	Tissue	Array	Overlap	Reference
main HD	GSE3790	26/38	cerebellum	GPL96	100%	[27]
		16/18	BA4 region of frontal cortex
		12/18	BA9 region of frontal cortex
		32/36	caudate nucleus
AD	GSE26927	7/11	entorhinal cortex	GPL6255	94.2%	[35]
ALS		9/10	cervical spinal cord
HD-II		10/9	ventral head of the caudate nucleus
MS		10/8	superior frontal gyri
PD		8/12	substantia nigra
SCHIZ		8/9	temporal cortex left, BA22 region
DM1	GSE7014	5/10	skeletal muscle	GPL570	100%	[81]
DM2	GSE7014	5/20	skeletal muscle	GPL570	100%	[81]
DMD	GSE6011	14/22	quadriceps muscle	GPL96	100%	[82]
DCM	GSE3585	5/7	heart	GPL96	100%	[83]
RCC	GSE781	5/12	kidney	GPL96	100%	[84]
GG	E-MEXP-1690	6/6	brain	GPL96	100%	[85]
Set	Accession	WT/HD	Tissue	Array	Overlap	Reference
Q80	GSE10263	3/3	striatum	GPL81	51.2%	[28]
Q150	GSE10263	4/4	striatum	GPL1261	81.9%
Q92	GSE7958	3/3 (3 mth)	striatum	GPL1261	81.9%
Q92	GSE7958	3/3 (18 mth)	striatum	GPL1261	81.9%
R6/2	GSE10263	9/9	striatum	GPL1261	81.9%
YAC128	GSE19677	4/4 (12 mth) 3/6 (24 mth)	striatum	GPL1261	81.9%	[24]

The abbreviations for the datasets are as follows: main HD = main Huntington’s disease dataset; AD = Alzheimer’s disease; ALS = Amyotrophic lateral sclerosis; HD-II = Huntington’s disease dataset 2; MS = multiple sclerosis; PD = Parkinson’s disease; SCHIZ = schizophrenia; DM1, DM2 = myotonic dystrophy type 1, type 2; DMD = Duchenne muscular dystrophy; DCM = dilated cardiomyopathy; RCC = renal cell carcinoma; GG = ganglioglioma; Q80 = Hdh4^80Q; Q150 = HdhQ150; Q92 = Hdh ^Q92. Accession is the accession number of the EMBL-EBI ArrayExpress, or NCBI Gene Expression Omnibus (GEO). Ctr/patient and WT/tg gives the sample numbers after outlier removal for control (ctr) or patient samples and wild type (WT) or HD mouse model samples (HD), respectively. For details of outlier removal procedure see materials and methods. Array lists the microarray type used for the particular study; for details see the GEO database. Overlap gives the percentage of genes, which are detected on the particular chip in comparison to the main HD array (GPL96).

ISSN: 1755-8794