Table 2. Summary of Microarray Profiling Studies.

Transgenic Mouse Models:
Study	Tissue Profiled	Form of mutant huntingtin	Comment
(Luthi-Carter et al., 2000)	R6/2 mouse striatum	Transgenic expression of human exon 1 with ∼150Q	1.7% of genes are changed, with decreases outnumbering increases by 3:1. Decreased genes include: neurotransmitters and receptors, second messengers, calcium homeostasis and nuclear receptors.
(Iannicola et al., 2000)	R6/1 whole brain	Transgenic expression of human exon 1 with ∼115Q	Whole brain mRNA hybridized to filters containing cDNA for 588 genes. 7 genes increased; 2 decreased.
(Chan et al., 2002)	Striatum from R6/2, N171-82Q, HD46, YAC72 transgenic mice	Transgenic mice expressing different lengths of human Htt	Mice with shorter fragments demonstrate more pronounced gene expression changes. Strength of conclusions undermined by the many differences in the models used.
(Luthi-Carter et al., 2002b)	Striatum of mouse models of HD, SCA-7, DRPLA, and SBMA	Different polyglutamine disease transgenes	Many shared gene changes bolster the idea that polyglutamine moiety is responsible for gene changes
(Ferrante et al., 2003)	R6/2 striatum	Transgenic expression of human exon 1 with ∼150Q	Treatment with the HDAC inhibitor sodium butyrate partially reverses transcriptional dysregulation
(Benn et al., 2005)	Striatum of NLS- and NES versions of R6 mouse lines	Transgenic expression of human exon 1 with ∼140Q	Nuclear localization produces more mor pronounced changes. R6/2 and R6/2 mice chare similar transcriptional profiles.
(Oyama et al., 2006)	Transgenic HD190QG mice	Transgenic expression of human exon 1 with 190Q, fused to eGFP	Overall pattern similar to that seen in R6/2 mice, additional ESTs identified. Identifies sodium channel beta4 subunit as downregulated, possible involvement in neurite retraction
(Morton et al., 2005a)	R6/2 mouse striatum	Transgenic expression of human exon 1 with ∼150Q	Treatment of with a combination of tacrine, moclobemide and creatine partially reverses gene expression abnormalities
(Desplats et al., 2006)	R6/1 mouse striatum	Transgenic expression of human exon 1 with ∼140Q	Pattern of downregulated genes explains striatal specificity
(Crocker et al., 2006)	R6/2 mouse striatum	Transgenic expression of human exon 1 with ∼150Q	170/15000 (1.1%) genes changed. More genes upregulated than downregulated.
Cell Models:
Study	Tissue Profiled	Form of mutant huntingtin	Comment
(Wyttenbach et al., 2001)	PC12 cells	Human exon 1, inducible expression, 23Q, or 74Q	Evidence of compromised CRE-mediated transcription, partially resuced by cAMP or forskolin.
(Sipione et al., 2002)	ST14a immortalized striatal cells	N-terminal 548-amino-acid huntingtin fragments with 26, 67, 105 or 118 glutamines	Inducible system allows for temporal resolution of gene changes. More genes decreased than increased. Cholesterol metabolism implicated.
(Kita et al., 2002)	PC12 cells	Stable Human exon 1 with 23Q or 74Q	126/1824 (6.9%) genes changed. Some of the genes with identified changes involved with cell death.
(Sugars et al., 2004)	PC12 cells	Exon 1, inducible	Disrupted pathways controlled by cAMP response element (CRE), retinoic acid response element, and nuclear factor kappaB,
(Apostol et al., 2006)	PC12 cells	Truncated form of human exon 1	85 genes increased, 53 genes decreased. Suggests activation of MAP kinase pathway.
Human:
Study	Tissue Profiled	Form of mutant huntingtin	Comment
(Borovecki et al., 2005)	Human peripheral blood cells	Mutant human HD alleles	More genes increased than decreased. Sets of genes could discriminate control, presymptomatic and symptomatic patients.
(Hodges et al., 2006)	Human HD brain	Mutant human HD alleles	Results remarkably similar to that seen in truncated transgenic mouse models. Gene changes most prominent in striatum and motor cortex, with few changes in cerebellum and none in frontal association cortex.