Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases

Li, Matthew D; Burns, Terry C; Morgan, Alexander A; Khatri, Purvesh

doi:10.1186/s40478-014-0093-y

Acta Neuropathologica Communications

Table 1 Summary of public gene expression data sets used in the discovery, validation, and secondary validation data set meta-analyses

From: Integrated multi-cohort transcriptional meta-analysis of neurodegenerative diseases

Disease		Accession #	Study first author	Year	Citation	Cases	Controls	Total samples	Tissue source
Discovery	ALS	GSE4595	Lederer	2007	[22]	11	9	20	Motor cortex
	ALS	GSE26927	Durrenberger	2012	[23]	10	10	20	Cervical spinal cord
	HD	GSE3790	Hodges	2006	[24]	19	16	35	Motor cortex
	HD	GSE26927	Durrenberger	2012	[23]	10	10	20	Ventral head of caudate nucleus
	PD	GSE7621	Lesnick	2007	[25]	16	9	25	Substantia nigra
	PD	E-MTAB812	Dumitriu	2012	[26]	27	26	53	Dorsolateral prefrontal cortex
	PD	GSE20291	Zhang	2005	[27]	15	20	35	Putamen
	AD	GSE29378	Miller	2013	[28]	16	16	32	Hippocampus (CA1)
	AD	GSE36980	Hokama	2013	[29]	15	12	27	Frontal cortex
	AD	GSE26927	Durrenberger	2012	[23]	11	7	18	Entorhinal cortex
TOTAL						150	135	285
Validation	HD	GSE33000	Zhu	2013	^a	157	155	312	Dorsolateral prefrontal cortex
	AD	GSE33000	Zhu	2013	^b	310	^c	310	Dorsolateral prefrontal cortex
	AD	GSE15222	Webster	2009	[30]	176	187	363	Various cortical regions
TOTAL						643	342	985
Secondary validation	PD	GSE26927	Durrenberger	2012	[23]	12	8	20	Substantia nigra
	PD	GSE20333	Grunblatt	2004	[31]	6	6	12	Substantia nigra
	PD	GSE20164	Hauser	2005	[32]	6	5	11	Substantia nigra
	PD	GSE20163	Zheng	2010	[16]	8	9	17	Substantia nigra
	PD	GSE8397	Moran	2006	[33]	9	7	16	Lateral substantia nigra
	PD	GSE7307	Roth	2008	^a	5	13	18	Putamen
	PD	GSE19587	Lewandowski	2010	[34]	6	5	11	Dorsal motor nucleus of Vagus nerve
	PD	GSE20146	Zheng	2010	[16]	10	10	20	Globus pallidus interna
	AD	GSE1297	Blalock	2004	[35]	22	9	31	Hippocampus
	AD	E-MEXP2280	Bronner	2009	[36]	5	5	10	Medial temporal lobe
	PiD	E-MEXP2280	Bronner	2009	[36]	5	^d	5	Medial temporal lobe
	PSP	E-MEXP2280	Bronner	2009	[36]	5	^d	5	Medial temporal lobe
	FTLD (C)	E-MEXP2280	Bronner	2009	[36]	5	^d	5	Medial temporal lobe
	FTLD-U (GRN+)	GSE13162	Chen-Plotkin	2008	[37]	6	8	14	Frontal cortex
	FTLD-U (GRN-)	GSE13162	Chen-Plotkin	2008	[37]	10	^e	10	Frontal cortex
TOTAL						120	85	205

See Additional file 1: Table S1 for individual sample accession numbers. ALS, amyotrophic lateral sclerosis; HD, Huntington’s disease; PD, Parkinson’s disease; AD, Alzheimer’s disease; PiD, classical Pick’s disease; PSP, progressive supranuclear palsy; FTLD, frontotemporal lobar dementia; FTLD (C), FTLD Constantinidis type C; FTLD-U, FTLD with ubiquitin- and TDP-43-positive inclusions; GRN+/–, progranulin mutation positive/negative. ^anot published yet; ^bpublished in part in [38]; ^csame control samples as the GSE33000 HD data; ^dsame control samples as the E-MEXP-2280 PiD data; ^esame control samples as the GSE13162 FTLD-U (GRN+) data.

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ISSN: 2051-5960

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