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Table 5 Microarray datasets used in this study

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

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 5/20 skeletal muscle
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%
3/3 (18 mth)
R6/2 GSE10263 9/9 striatum GPL1261 81.9%
YAC128 GSE19677 4/4 (12 mth) 3/6 (24 mth) striatum GPL1261 81.9% [24]
  1. 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 = Hdh480Q; 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).