Gene expression profiling in human neurodegenerative disease (original) (raw)

• Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470 (1995).
  CAS PubMed Google Scholar
• Saris, C. G. et al. Weighted gene co-expression network analysis of the peripheral blood from amyotrophic lateral sclerosis patients. BMC Genomics 10, 405 (2009).
  PubMed PubMed Central Google Scholar
• Offen, D. et al. Spinal cord mRNA profile in patients with ALS: comparison with transgenic mice expressing the human SOD-1 mutant. J. Mol. Neurosci. 38, 85–93 (2009).
  CAS PubMed Google Scholar
• Wang, X. S., Simmons, Z., Liu, W., Boyer, P. J. & Connor, J. R. Differential expression of genes in amyotrophic lateral sclerosis revealed by profiling the post mortem cortex. Amyotroph. Lateral Scler. 7, 201–210 (2006).
  CAS PubMed Google Scholar
• Lederer, C. W., Torrisi, A., Pantelidou, M., Santama, N. & Cavallaro, S. Pathways and genes differentially expressed in the motor cortex of patients with sporadic amyotrophic lateral sclerosis. BMC Genomics 8, 26 (2007).
  PubMed PubMed Central Google Scholar
• Ferraiuolo, L., Kirby, J., Grierson, A. J., Sendtner, M. & Shaw, P. J. Molecular pathways of motor neuron injury in amyotrophic lateral sclerosis. Nat. Rev. Neurol. 7, 616–630 (2011).
  CAS PubMed Google Scholar
• Kirby, J. et al. Phosphatase and tensin homologue/protein kinase B pathway linked to motor neuron survival in human superoxide dismutase 1-related amyotrophic lateral sclerosis. Brain 134, 506–517 (2011).
  PubMed PubMed Central Google Scholar
• Jiang, Y. M. et al. Gene expression profile of spinal motor neurons in sporadic amyotrophic lateral sclerosis. Ann. Neurol. 57, 236–251 (2005).
  CAS PubMed Google Scholar
• Rabin, S. J. et al. Sporadic ALS has compartment-specific aberrant exon splicing and altered cell-matrix adhesion biology. Hum. Mol. Genet. 19, 313–328 (2010).
  CAS PubMed Google Scholar
• Cox, L. E. et al. Mutations in CHMP2B in lower motor neuron predominant amyotrophic lateral sclerosis (ALS). PLoS ONE 5, e9872 (2010).
  PubMed PubMed Central Google Scholar
• Hewitt, C. et al. Novel FUS/TLS mutations and pathology in familial and sporadic amyotrophic lateral sclerosis. Arch. Neurol. 67, 455–461 (2010).
  PubMed Google Scholar
• Kirby, J. et al. Broad clinical phenotypes associated with TAR-DNA binding protein (TARDBP) mutations in amyotrophic lateral sclerosis. Neurogenetics 11, 217–225 (2010).
  CAS PubMed Google Scholar
• Kirby, J. et al. Mutant SOD1 alters the motor neuronal transcriptome: implications for familial ALS. Brain 128, 1686–1706 (2005).
  PubMed Google Scholar
• Ferraiuolo, L. et al. Microarray analysis of the cellular pathways involved in the adaptation to and progression of motor neuron injury in the SOD1 G93A mouse model of familial ALS. J. Neurosci. 27, 9201–9219 (2007).
  CAS PubMed PubMed Central Google Scholar
• Zhang, R. et al. Gene expression profiling in peripheral blood mononuclear cells from patients with sporadic amyotrophic lateral sclerosis (sALS). J. Neuroimmunol. 230, 114–123 (2011).
  CAS PubMed Google Scholar
• Mougeot, J.-L., Li, Z., Price, A., Wright, F. & Brooks, B. Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathway. BMC Med. Genomics 4, 74 (2011).
  CAS PubMed PubMed Central Google Scholar
• Pradat, P. F. et al. Muscle gene expression is a marker of amyotrophic lateral sclerosis severity. Neurodegen. Dis. 9, 38–52 (2012).
  Google Scholar
• Shtilbans, A. et al. Differential gene expression in patients with amyotrophic lateral sclerosis. Amyotroph. Lateral Scler. 12, 250–256 (2011).
  CAS PubMed Google Scholar
• Scherzer, C. R. et al. Molecular markers of early Parkinson's disease based on gene expression in blood. Proc. Natl Acad. Sci. USA 104, 955–960 (2007).
  CAS PubMed PubMed Central Google Scholar
• Zheng, B. et al. PGC-1α, a potential therapeutic target for early intervention in Parkinson's disease. Sci. Transl. Med. 2, 52ra73 (2010).
  PubMed PubMed Central Google Scholar
• Elstner, M. et al. Expression analysis of dopaminergic neurons in Parkinson's disease and aging links transcriptional dysregulation of energy metabolism to cell death. Acta Neuropathol. 122, 75–86 (2011).
  CAS PubMed Google Scholar
• Shin, J.-H. et al. PARIS (ZNF746) repression of PGC-1α contributes to neurodegeneration in Parkinson's disease. Cell 144, 689–702 (2011).
  CAS PubMed PubMed Central Google Scholar
• Papapetropoulos, S. et al. Multiregional gene expression profiling identifies MRPS6 as a possible candidate gene for Parkinson's disease. Gene Expr. 13, 205–215 (2006).
  CAS PubMed Google Scholar
• Moran, L. et al. Whole genome expression profiling of the medial and lateral substantia nigra in Parkinson's disease. Neurogenetics 7, 1–11 (2006).
  CAS PubMed Google Scholar
• Hauser, M. A. et al. Expression profiling of substantia nigra in Parkinson disease, progressive supranuclear palsy, and frontotemporal dementia with parkinsonism. Arch. Neurol. 62, 917–921 (2005).
  PubMed Google Scholar
• Zhang, Y., James, M., Middleton, F. A. & Davis, R. L. Transcriptional analysis of multiple brain regions in Parkinson's disease supports the involvement of specific protein processing, energy metabolism, and signaling pathways, and suggests novel disease mechanisms. Am. J. Med. Genet. B Neuropsychiatr. Genet. 137B, 5–16 (2005).
  PubMed Google Scholar
• Vogt, I. R. et al. Transcriptional changes in multiple system atrophy and Parkinson's disease putamen. Exp. Neurol. 199, 465–478 (2006).
  CAS PubMed Google Scholar
• Naydenov, A., Vassoler, F., Luksik, A., Kaczmarska, J. & Konradi, C. Mitochondrial abnormalities in the putamen in Parkinson's disease dyskinesia. Acta Neuropathol. 120, 623–631 (2010).
  CAS PubMed PubMed Central Google Scholar
• Botta-Orfila, T. et al. Microarray expression analysis in idiopathic and _LRRK2_-associated Parkinson's disease. Neurobiol. Dis. 45, 462–468 (2012).
  CAS PubMed Google Scholar
• Durrenberger, P. et al. Inflammatory pathways in Parkinson's disease; a BNE microarray study. Parkinson Dis. 2012, 214714 (2012).
  Google Scholar
• Bossers, K. et al. Analysis of gene expression in Parkinson's disease: possible involvement of neurotrophic support and axon guidance in dopaminergic cell death. Brain Pathol. 19, 91–107 (2009).
  CAS PubMed Google Scholar
• Miller, R. M. et al. Robust dysregulation of gene expression in substantia nigra and striatum in Parkinson's disease. Neurobiol. Dis. 21, 305–313 (2006).
  CAS PubMed Google Scholar
• Duke, D., Moran, L., Pearce, R. & Graeber, M. The medial and lateral substantia nigra in Parkinson's disease: mRNA profiles associated with higher brain tissue vulnerability. Neurogenetics 8, 83–94 (2007).
  CAS PubMed Google Scholar
• Fearnley, J. M. & Lees, A. J. Ageing and Parkinson's disease: substantia nigra regional selectivity. Brain 114, 2283–2301 (1991).
  PubMed Google Scholar
• Zhou, C., Huang, Y. & Przedborski, S. Oxidative stress in Parkinson's disease. Ann. NY Acad. Sci. 1147, 93–104 (2008).
  CAS PubMed Google Scholar
• Rideout, H. J., Larsen, K. E., Sulzer, D. & Stefanis, L. Proteasomal inhibition leads to formation of ubiquitin/α-synuclein-immunoreactive inclusions in PC12 cells. J. Neurochem. 78, 899–908 (2001).
  CAS PubMed Google Scholar
• Vila, M. & Przedborski, S. Targeting programmed cell death in neurodegenerative diseases. Nat. Rev. Neurosci. 4, 365–375 (2003).
  CAS PubMed Google Scholar
• Ved, R. et al. Similar patterns of mitochondrial vulnerability and rescue induced by genetic modification of α-synuclein, parkin, and DJ-1 in Caenorhabditis elegans. J. Biol. Chem. 280, 42655–42668 (2005).
  CAS PubMed Google Scholar
• Dawson, T. M. & Dawson, V. L. Molecular pathways of neurodegeneration in Parkinson's disease. Science 302, 819–822 (2003).
  CAS PubMed Google Scholar
• Quigley, P. M., Korotkov, K., Baneyx, F. & Hol, W. G. The 1.6-Å crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad. Proc. Natl Acad. Sci. USA 100, 3137–3142 (2003).
  CAS PubMed PubMed Central Google Scholar
• Moran, L. et al. Analysis of alpha-synuclein, dopamine and parkin pathways in neuropathologically confirmed parkinsonian nigra. Acta Neuropathol. 113, 253–263 (2007).
  CAS PubMed Google Scholar
• Duke, D. et al. Transcriptome analysis reveals link between proteasomal and mitochondrial pathways in Parkinson's disease. Neurogenetics 7, 139–148 (2006).
  CAS PubMed Google Scholar
• Mortiboys, H., Johansen, K., Aasly, J. & Bandmann, O. Mitochondrial impairment in patients with Parkinson disease with the G2019S mutation in LRRK2. Neurology 75, 2017–2020 (2010).
  CAS PubMed Google Scholar
• Cantuti-Castelvetri, I. et al. Effects of gender on nigral gene expression and Parkinson disease. Neurobiol. Dis. 26, 606–614 (2007).
  CAS PubMed PubMed Central Google Scholar
• Simunovic, F. et al. Gene expression profiling of substantia nigra dopamine neurons: further insights into Parkinson's disease pathology. Brain 132, 1795–1809 (2009).
  PubMed Google Scholar
• Stamper, C. et al. Neuronal gene expression correlates of Parkinson's disease with dementia. Mov. Disord. 23, 1588–1595 (2008).
  PubMed PubMed Central Google Scholar
• Simunovic, F., Yi, M., Wang, Y., Stephens, R. & Sonntag, K. C. Evidence for gender-specific transcriptional profiles of nigral dopamine neurons in Parkinson disease. PLoS ONE 5, e8856 (2010).
  PubMed PubMed Central Google Scholar
• Surmeier, D. J. Calcium, ageing, and neuronal vulnerability in Parkinson's disease. Lancet Neurol. 6, 933–938 (2007).
  CAS PubMed Google Scholar
• Shehadeh, L. A. et al. SRRM2, a potential blood biomarker revealing high alternative splicing in Parkinson's disease. PLoS ONE 5, e9104 (2010).
  PubMed PubMed Central Google Scholar
• Mar, J. C. et al. Variance of gene expression identifies altered network constraints in neurological disease. PLoS Genet. 7, e1002207 (2011).
  CAS PubMed PubMed Central Google Scholar
• Matigian, N. et al. Disease-specific, neurosphere-derived cells as models for brain disorders. Dis. Model. Mech. 3, 785–798 (2010).
  CAS PubMed Google Scholar
• Mutez, E. et al. Transcriptional profile of Parkinson blood mononuclear cells with LRRK2 mutation. Neurobiol. Aging 32, 1839–1848 (2011).
  CAS PubMed Google Scholar
• Parachikova, A. et al. Inflammatory changes parallel the early stages of Alzheimer disease. Neurobiol. Aging 28, 1821–1833 (2007).
  CAS PubMed Google Scholar
• Tan, M. G. et al. Genome wide profiling of altered gene expression in the neocortex of Alzheimer's disease. J. Neurosci. Res. 88, 1157–1169 (2010).
  CAS PubMed Google Scholar
• Williams, C. et al. Transcriptome analysis of synaptoneurosomes identifies neuroplasticity genes overexpressed in incipient Alzheimer's disease. PLoS ONE 4, e4936 (2009).
  PubMed PubMed Central Google Scholar
• Xu, P.-T. et al. Differences in apolipoprotein E3/3 and E4/4 allele-specific gene expression in hippocampus in Alzheimer disease. Neurobiol. Dis. 21, 256–275 (2006).
  CAS PubMed Google Scholar
• Emilsson, L., Saetre, P. & Jazin, E. Alzheimer's disease: mRNA expression profiles of multiple patients show alterations of genes involved with calcium signaling. Neurobiol. Dis. 21, 618–625 (2006).
  CAS PubMed Google Scholar
• Haroutunian, V., Katsel, P. & Schmeidler, J. Transcriptional vulnerability of brain regions in Alzheimer's disease and dementia. Neurobiol. Aging 30, 561–573 (2009).
  CAS PubMed Google Scholar
• Katsel, P., Li, C. & Haroutunian, V. Gene expression alterations in the sphingolipid metabolism pathways during progression of dementia and Alzheimer's disease: a shift toward ceramide accumulation at the earliest recognizable stages of Alzheimer's disease? Neurochem. Res. 32, 845–856 (2007).
  CAS PubMed Google Scholar
• Katsel, P., Tan, W. & Haroutunian, V. Gain in brain immunity in the oldest-old differentiates cognitively normal from demented individuals. PLoS ONE 4, e7642 (2009).
  PubMed PubMed Central Google Scholar
• Umemura, K. et al. Autotaxin expression is enhanced in frontal cortex of Alzheimer-type dementia patients. Neurosci. Lett. 400, 97–100 (2006).
  CAS PubMed Google Scholar
• Weeraratna, A. T. et al. Alterations in immunological and neurological gene expression patterns in Alzheimer's disease tissues. Exp. Cell Res. 313, 450–461 (2007).
  CAS PubMed Google Scholar
• Bronner, I. F. et al. Comprehensive mRNA expression profiling distinguishes tauopathies and identifies shared molecular pathways. PLoS ONE 4, e6826 (2009).
  PubMed PubMed Central Google Scholar
• Bossers, K. et al. Concerted changes in transcripts in the prefrontal cortex precede neuropathology in Alzheimer's disease. Brain 133, 3699–3723 (2010).
  PubMed Google Scholar
• Horesh, Y., Katsel, P., Haroutunian, V. & Domany, E. Gene expression signature is shared by patients with Alzheimer's disease and schizophrenia at the superior temporal gyrus. Eur. J. Neurol. 18, 410–424 (2011).
  CAS PubMed Google Scholar
• Youn, H. et al. Kalirin is under-expressed in Alzheimer's disease hippocampus. J. Alzheimers Dis. 11, 385–397 (2007).
  CAS PubMed Google Scholar
• Wang, S., Qaisar, U., Yin, X. & Grammas, P. Gene expression profiling in Alzheimer's disease brain microvessels. J. Alzheimers Dis. http://dx.doi.org/10.3233/JAD-2012-120454.
• Tollervey, J. R. et al. Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res. 21, 1572–1582 (2011).
  CAS PubMed PubMed Central Google Scholar
• Kuchibhotla, K. V. et al. Aβ plaques lead to aberrant regulation of calcium homeostasis in vivo resulting in structural and functional disruption of neuronal networks. Neuron 59, 214–225 (2008).
  CAS PubMed PubMed Central Google Scholar
• Guo, Q. et al. Alzheimer's PS-1 mutation perturbs calcium homeostasis and sensitizes PC12 cells to death induced by amyloid peptide. Neuroreport 8, 379–383 (1996).
  CAS PubMed Google Scholar
• Camandola, S. & Mattson, M. P. Aberrant subcellular neuronal calcium regulation in aging and Alzheimer's disease. Biochim. Biophys. Acta 1813, 965–973 (2011).
  CAS PubMed Google Scholar
• Berchtold, N. C. et al. Gene expression changes in the course of normal brain aging are sexually dimorphic. Proc. Natl Acad. Sci. USA 105, 15605–15610 (2008).
  CAS PubMed PubMed Central Google Scholar
• Saetre, P., Jazin, E. & Emilsson, L. Age-related changes in gene expression are accelerated in Alzheimer's disease. Synapse 65, 971–974 (2011).
  CAS PubMed Google Scholar
• Masliah, E. et al. Altered expression of synaptic proteins occurs early during progression of Alzheimer's disease. Neurology 56, 127–129 (2001).
  CAS PubMed Google Scholar
• Giuditta, A. et al. Local gene expression in axons and nerve endings: the glia–neuron unit. Physiol. Rev. 88, 515–555 (2008).
  CAS PubMed Google Scholar
• Liang, W. S. et al. Altered neuronal gene expression in brain regions differentially affected by Alzheimer's disease: a reference data set. Physiol. Genomics 33, 240–256 (2008).
  CAS PubMed Google Scholar
• Liang, W. S. et al. Alzheimer's disease is associated with reduced expression of energy metabolism genes in posterior cingulate neurons. Proc. Natl Acad. Sci. USA 105, 4441–4446 (2008).
  CAS PubMed PubMed Central Google Scholar
• Dunckley, T. et al. Gene expression correlates of neurofibrillary tangles in Alzheimer's disease. Neurobiol. Aging 27, 1359–1371 (2006).
  CAS PubMed Google Scholar
• Alexander, G. E., Chen, K., Pietrini, P., Rapoport, S. I. & Reiman, E. M. Longitudinal PET evaluation of cerebral metabolic decline in dementia: a potential outcome measure in Alzheimer's disease treatment studies. Am. J. Psychiatry 159, 738–745 (2002).
  PubMed Google Scholar
• Minoshima, S. et al. Metabolic reduction in the posterior cingulate cortex in very early Alzheimer's disease. Ann. Neurol. 42, 85–94 (1997).
  CAS PubMed Google Scholar
• Ray, M. & Zhang, W. Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks. BMC Syst. Biol. 4, 136 (2010).
  PubMed PubMed Central Google Scholar
• Liu, Z.-P., Wang, Y., Zhang, X.-S. & Chen, L. Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer's disease brains. BMC Syst. Biol. 4, S11 (2010).
  PubMed PubMed Central Google Scholar
• Ray, M., Ruan, J. & Zhang, W. Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases. Genome Biol. 9, R148 (2008).
  PubMed PubMed Central Google Scholar
• Gorelick, P. B. et al. Vascular contributions to cognitive impairment and dementia. Stroke 42, 2672–2713 (2011).
  PubMed PubMed Central Google Scholar
• Helbecque, N. & Amouyel, P. Commonalities between genetics of cardiovascular disease and neurodegenerative disorders. Curr. Opin. Lipidol. 15, 121–127 (2004).
  CAS PubMed Google Scholar
• Simpson, J. E. et al. Microarray analysis of the astrocyte transcriptome in the aging brain: relationship to Alzheimer's pathology and APOE genotype. Neurobiol. Aging 32, 1795–1807 (2011).
  CAS PubMed Google Scholar
• Strittmatter, W. J. et al. Apolipoprotein E: high-avidity binding to β-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease. Proc. Natl Acad. Sci. USA 90, 1977–1981 (1993).
  CAS PubMed PubMed Central Google Scholar
• Maes, O. C. et al. Transcriptional profiling of Alzheimer blood mononuclear cells by microarray. Neurobiol. Aging 28, 1795–1809 (2007).
  CAS PubMed Google Scholar
• Nagasaka, Y. et al. A unique gene expression signature discriminates familial Alzheimer's disease mutation carriers from their wild-type siblings. Proc. Natl Acad. Sci. USA 102, 14854–14859 (2005).
  CAS PubMed PubMed Central Google Scholar
• Calciano, M. A., Zhou, W., Snyder, P. J. & Einstein, R. Drug treatment of Alzheimer's disease patients leads to expression changes in peripheral blood cells. Alzheimers Dement. 6, 386–393 (2010).
  CAS PubMed Google Scholar
• Booij, B. B. et al. A gene expression pattern in blood for the early detection of Alzheimer's disease. J. Alzheimers Dis. 23, 109–119 (2011).
  CAS PubMed Google Scholar
• Kálmán, J. et al. Gene expression profile analysis of lymphocytes from Alzheimer's patients. Psychiatr. Genet. 15, 1–6 (2005).
  PubMed Google Scholar
• Fehlbaum-Beurdeley, P. et al. Toward an Alzheimer's disease diagnosis via high-resolution blood gene expression. Alzheimers Dement. 6, 25–38 (2010).
  CAS PubMed Google Scholar
• Chen, K.-D. et al. Gene expression profiling of peripheral blood leukocytes identifies and validates ABCB1 as a novel biomarker for Alzheimer's disease. Neurobiol. Dis. 43, 698–705 (2011).
  CAS PubMed Google Scholar
• Rye, P. D. et al. A novel blood test for the early detection of Alzheimer's disease. J. Alzheimers Dis. 23, 121–129 (2011).
  CAS PubMed Google Scholar
• Scherzer, C. et al. Loss of apolipoprotein E receptor LR11 in Alzheimer disease. Arch. Neurol. 61, 1200–1205 (2004).
  PubMed Google Scholar
• Lee, J., Barral, S. & Reitz, C. The neuronal sortilin-related receptor gene SORL1 and late-onset Alzheimer's disease. Curr. Neurol. Neurosci. Rep. 8, 384–391 (2008).
  CAS PubMed PubMed Central Google Scholar
• Sutherland, G. T., Janitz, M. & Kril, J. J. Understanding the pathogenesis of Alzheimer's disease: will RNA-Seq realize the promise of transcriptomics? J. Neurochem. 116, 937–946 (2011).
  CAS PubMed Google Scholar
• Emmert-Buck, M. R. et al. Laser capture microdissection. Science 274, 998–1001 (1996).
  CAS PubMed Google Scholar
• Sutherland, G. T. et al. A cross-study transcriptional analysis of Parkinson's disease. PLoS ONE 4, e4955 (2009).
  PubMed PubMed Central Google Scholar
• Casale, V., Oneda, R., Lavezzi, A. M. & Matturri, L. Optimisation of postmortem tissue preservation and alternative protocol for serotonin transporter gene polymorphisms amplification in SIDS and SIUD cases. Exp. Mol. Pathol. 88, 202–205 (2010).
  CAS PubMed Google Scholar
• Durrenberger, P. F. et al. Effects of antemortem and postmortem variables on human brain mRNA quality: a BrainNet Europe study. J. Neuropathol. Exp. Neurol. 69, 70–81 (2010).
  PubMed Google Scholar
• Strand, C., Enell, J., Hedenfalk, I. & Ferno, M. RNA quality in frozen breast cancer samples and the influence on gene expression analysis—a comparison of three evaluation methods using microcapillary electrophoresis traces. BMC Mol. Biol. 8, 38 (2007).
  PubMed PubMed Central Google Scholar
• Schroeder, A. et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol. Biol. 7, 3 (2006).
  PubMed PubMed Central Google Scholar
• Copois, V. et al. Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J. Biotechnol. 127, 549–559 (2007).
  CAS PubMed Google Scholar
• Tan, P. K., et al. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31, 5676–5684 (2003).
  CAS PubMed PubMed Central Google Scholar
• MAQC Consortium et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotech. 24, 1151–1161 (2006).
• Posekany, A., Felsenstein, K. & Sykacek, P. Biological assessment of robust noise models in microarray data analysis. Bioinformatics 27, 807–814 (2011).
  CAS PubMed PubMed Central Google Scholar
• Stekel, D. Microarray Bioinformatics 110–138 (Cambridge University Press, Cambridge, UK, 2003).
  Google Scholar
• Storey, J. D., Dai, J. Y. & Leek, J. T. The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments. Biostatistics 8, 414–432 (2007).
  PubMed Google Scholar
• Hosack, D., Dennis, G., Sherman, B., Lane, H. & Lempicki, R. Identifying biological themes within lists of genes with EASE. Genome Biol. 4, R70 (2003).
  PubMed PubMed Central Google Scholar
• Smyth, G. K. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article 3 (2004).
  Google Scholar
• Liu, X., Milo, M., Lawrence, N. D. & Rattray, M. Probe-level measurement error improves accuracy in detecting differential gene expression. Bioinformatics 22, 2107–2113 (2006).
  CAS PubMed Google Scholar
• Blencowe, B. J., Ahmad, S. & Lee, L. J. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev. 23, 1379–1386 (2009).
  CAS PubMed Google Scholar
• Yamamoto, M. L. et al. Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis. Blood 113, 3363–3370 (2009).
  CAS PubMed PubMed Central Google Scholar
• Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956–960 (2008).
  CAS PubMed Google Scholar
• Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).
  CAS PubMed Google Scholar
• Metzker, M. L. Sequencing technologies—the next generation. Nat. Rev. Genet. 11, 31–46 (2010).
  CAS PubMed Google Scholar
• Tariq, M. A., Kim, H. J., Jejelowo, O. & Pourmand, N. Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res. http://dx.doi.org/10.1093/nar/gkr547.
• Łabaj, P. P. et al. Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics 27, i383–i391 (2011).
  PubMed PubMed Central Google Scholar
• Pascale, F.-B. et al. Toward an Alzheimer's disease diagnosis via high-resolution blood gene expression. Alzheimers Dement. 6, 25–38 (2010).
  Google Scholar
• Kaklamani, V. A genetic signature can predict prognosis and response to therapy in breast cancer: oncotype DX. Expert Rev. Mol. Diagn. 6, 803–809 (2006).
  CAS PubMed Google Scholar
• Shi, L. et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat. Biotechnol. 28, 827–838 (2010).
  CAS PubMed Google Scholar
• Rottenberg, S. et al. Impact of intertumoral heterogeneity on predicting chemotherapy response of BRCA1-deficient mammary tumors. Cancer Res. 72, 2350–2361 (2012).
  CAS PubMed PubMed Central Google Scholar
• Ein-Dor, L., Kela, I., Getz, G., Givol, D. & Domany, E. Outcome signature genes in breast cancer: is there a unique set? Bioinformatics 21, 171–178 (2005).
  CAS PubMed Google Scholar
• Ein-Dor, L., Zuk, O. & Domany, E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc. Natl Acad. Sci. USA 103, 5923–5928 (2006).
  CAS PubMed PubMed Central Google Scholar
• Cabeza-Arvelaiz, Y. et al. Analysis of striatal transcriptome in mice overexpressing human wild-type alpha-synuclein supports synaptic dysfunction and suggests mechanisms of neuroprotection for striatal neurons. Mol. Neurodegen. 6, 83 (2011).
  CAS Google Scholar
• Bredesen, D. E., Rao, R. V. & Mehlen, P. Cell death in the nervous system. Nature 443, 796–802 (2006).
  CAS PubMed PubMed Central Google Scholar
• Grünblatt, E. Commonalities in the genetics of Alzheimer's disease and Parkinson's disease. Expert Rev. Neurother. 8, 1865–1877 (2008).
  PubMed Google Scholar
• van Es, M. A. et al. Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis. Ann. Neurol. 70, 964–973 (2011).
  CAS PubMed PubMed Central Google Scholar