Genome-wide atlas of gene expression in the adult mouse brain

Zapala, M. A. et al. Adult mouse brain gene expression patterns bear an embryologic imprint. Proc. Natl Acad. Sci. USA 102, 10357–10362 (2005)

Datson, N. A., van der Perk, J., de Kloet, E. R. & Vreugdenhil, E. Expression profile of 30,000 genes in rat hippocampus using SAGE. Hippocampus 11, 430–444 (2001)

Sandberg, R. et al. Regional and strain-specific gene expression mapping in the adult mouse brain. Proc. Natl Acad. Sci. USA 97, 11038–11043 (2000)

Siddiqui, A. S. et al. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc. Natl Acad. Sci. USA 102, 18485–18490 (2005)

Kamme, F. et al. Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity. J. Neurosci. 23, 3607–3615 (2003)

Sugino, K. et al. Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nature Neurosci. 9, 99–107 (2006)

Markram, H. et al. Interneurons of the neocortical inhibitory system. Nature Rev. Neurosci. 5, 793–807 (2004)

Toledo-Rodriguez, M., Goodman, P., Illic, M., Wu, C. & Markram, H. Neuropeptide and calcium-binding protein gene expression profiles predict neuronal anatomical type in the juvenile rat. J. Physiol. (Lond.) 567, 401–413 (2005)

Monyer, H. & Markram, H. Interneuron diversity series: Molecular and genetic tools to study GABAergic interneuron diversity and function. Trends Neurosci. 27, 90–97 (2004)

Christiansen, J. H. et al. EMAGE: a spatial database of gene expression patterns during mouse embryo development. Nucleic Acids Res. 34, D637–D641 (2006)

Gong, S. et al. A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425, 917–925 (2003)

Visel, A., Thaller, C. & Eichele, G. GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 32, D552–D556 (2004)

Gray, P. A. et al. Mouse brain organization revealed through direct genome-scale TF expression analysis. Science 306, 2255–2257 (2004)

Magdaleno, S. et al. BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol. 4, e86 (2006)

Boguski, M. S. & Jones, A. R. Neurogenomics: at the intersection of neurobiology and genome sciences. Nature Neurosci. 7, 429–433 (2004)

Dennis, G. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, P3 (2003)

Kirkwood, A., Rioult, M. C. & Bear, M. F. Experience-dependent modification of synaptic plasticity in visual cortex. Nature 381, 526–528 (1996)

Elias, C. F. et al. Characterization of CART neurons in the rat and human hypothalamus. J. Comp. Neurol. 432, 1–19 (2001)

Heuer, H. et al. Connective tissue growth factor: a novel marker of layer VII neurons in the rat cerebral cortex. Neuroscience 119, 43–52 (2003)

Zola-Morgan, S., Squire, L. R. & Amaral, D. G. Human amnesia and the medial temporal region: enduring memory impairment following a bilateral lesion limited to field CA1 of the hippocampus. J. Neurosci. 6, 2950–2967 (1986)

Scoville, W. B. & Milner, B. Loss of recent memory after bilateral hippocampal lesions. 1957. J. Neuropsychiatry Clin. Neurosci. 12, 103–113 (2000)

Lorente de Nó, R. Studies on the structure of the cerebral cortex. II. Continuation of the study of the ammonic system. J. Psychol. Neurol. (Lpz.) 46, 113–177 (1934)

Amaral, D. G. & Witter, M. P. The three-dimensional organization of the hippocampal formation: a review of anatomical data. Neuroscience 31, 571–591 (1989)

Ishizuka, N., Weber, J. & Amaral, D. G. Organization of intrahippocampal projections originating from CA3 pyramidal cells in the rat. J. Comp. Neurol. 295, 580–623 (1990)

Tole, S., Christian, C. & Grove, E. A. Early specification and autonomous development of cortical fields in the mouse hippocampus. Development 124, 4959–4970 (1997)

Lein, E. S., Zhao, X. & Gage, F. H. Defining a molecular atlas of the hippocampus using DNA microarrays and high-throughput in situ hybridization. J. Neurosci. 24, 3879–3889 (2004)

Yamagata, M., Sanes, J. R. & Weiner, J. A. Synaptic adhesion molecules. Curr. Opin. Cell Biol. 15, 621–632 (2003)

Small, S. A. The longitudinal axis of the hippocampal formation: its anatomy, circuitry, and role in cognitive function. Rev. Neurosci. 13, 183–194 (2002)

Moser, M. B. & Moser, E. I. Functional differentiation in the hippocampus. Hippocampus 8, 608–619 (1998)

Bannerman, D. M. et al. Regional dissociations within the hippocampus—memory and anxiety. Neurosci. Biobehav. Rev. 28, 273–283 (2004)

Voogd, J., Hess, D. & Marani, E. The Parasagittal Zonation of the Cerebellar Cortex in Cat and Monkey: Topography, Distribution of Acetylcholinesterase, and Development (ed. King, E. S.) (Liss, New York, 1987)

Herrup, K. & Kuemerle, B. The compartmentalization of the cerebellum. Annu. Rev. Neurosci. 20, 61–90 (1997)

Hawkes, R. & Herrup, K. Aldolase C/zebrin II and the regionalization of the cerebellum. J. Mol. Neurosci. 6, 147–158 (1995)

Gravel, C. & Hawkes, R. Parasagittal organization of the rat cerebellar cortex: direct comparison of Purkinje cell compartments and the organization of the spinocerebellar projection. J. Comp. Neurol. 291, 79–102 (1990)

Blackshaw, S. & Snyder, S. H. Encephalopsin: a novel mammalian extraretinal opsin discretely localized in the brain. J. Neurosci. 19, 3681–3690 (1999)

Eberwine, J., Belt, B., Kacharmina, J. E. & Miyashiro, K. Analysis of subcellularly localized mRNAs using in situ hybridization, mRNA amplification, and expression profiling. Neurochem. Res. 27, 1065–1077 (2002)

Kang, H. & Schuman, E. M. A requirement for local protein synthesis in neurotrophin-induced hippocampal synaptic plasticity. Science 273, 1402–1406 (1996)

Huber, K. M., Kayser, M. S. & Bear, M. F. Role for rapid dendritic protein synthesis in hippocampal mGluR-dependent long-term depression. Science 288, 1254–1257 (2000)

Burgin, K. E. et al. In situ hybridization histochemistry of Ca2+/calmodulin-dependent protein kinase in developing rat brain. J. Neurosci. 10, 1788–1798 (1990)

Trapp, B. D. et al. Spatial segregation of mRNA encoding myelin-specific proteins. Proc. Natl Acad. Sci. USA 84, 7773–7777 (1987)

Kindler, S., Wang, H., Richter, D. & Tiedge, H. RNA transport and local control of translation. Annu. Rev. Cell Dev. Biol. 21, 223–245 (2005)

Carninci, P. et al. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005)

Panda, S. et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109, 307–320 (2002)

Vavouri, T. & Elgar, G. Prediction of cis-regulatory elements using binding site matrices—the successes, the failures and the reasons for both. Curr. Opin. Genet. Dev. 15, 395–402 (2005)

Luquet, S., Perez, F. A., Hnasko, T. S. & Palmiter, R. D. NPY/AgRP neurons are essential for feeding in adult mice but can be ablated in neonates. Science 310, 683–685 (2005)

Lechner, H. A., Lein, E. S. & Callaway, E. M. A genetic method for selective and quickly reversible silencing of Mammalian neurons. J. Neurosci. 22, 5287–5290 (2002)

Yoshihara, Y. et al. A genetic approach to visualization of multisynaptic neural pathways using plant lectin transgene. Neuron 22, 33–41 (1999)

DeFalco, J. et al. Virus-assisted mapping of neural inputs to a feeding center in the hypothalamus. Science 291, 2608–2613 (2001)

Brecht, M. et al. Novel approaches to monitor and manipulate single neurons in vivo. J. Neurosci. 24, 9223–9227 (2004)

Ng, L. et al. Neuroinformatics for genome-wide 3-D gene expression mapping in the mouse brain. IEEE Trans. Comput. Biol. Bioinform. (in the press).

Thompson, P. M. & Toga, A. W. in Handbook of Medical Imaging: Processing and Analysis (ed. Bankman, I. N.) (Academic Press, San Diego, 2000)

Viola, P. & Wells, W. M. Alignment by maximization of mutual information. Int. J. Comput. Vis. 24, 137–154 (1997)

Chan, T. F. & Shen, J. Image Processing and Analysis: Variation, PDE, Wavelet, and Stochastic Methods (Society for Industrial and Applied Mathematics, Philadelphia, 2005)

Lein, E. S., Callaway, E. M., Albright, T. D. & Gage, F. H. Redefining the boundaries of the hippocampal CA2 subfield in the mouse using gene expression and 3-dimensional reconstruction. J. Comp. Neurol. 485, 1–10 (2005)

Swanson, L. W. Brain Maps: Structure of the Rat Brain (Elsevier, Amsterdam, 2004)