The DOI matches its Crossref record; 57 of the 58 references it cites were found in a registry or an index.
Genome-wide atlas of gene expression in the adult mouse brain
Abstract
Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive digital atlas containing the expression patterns of approximately 20,000 genes in the adult mouse brain. Data were generated using automated high-throughput procedures for in situ hybridization and data acquisition, and are publicly accessible online. Newly developed image-based informatics tools allow global genome-scale structural analysis and cross-correlation, as well as identification of regionally enriched genes. Unbiased fine-resolution analysis has identified highly specific cellular markers as well as extensive evidence of cellular heterogeneity not evident in classical neuroanatomical atlases. This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“In order to independently validate our findings about the spatial distribution of astrocytes (Figure S5C), we analyzed in situ hybridization images of marker genes obtained from the Allen Mouse Brain Atlas”
From Molecular Architecture of the Mouse Nervous System (2018) · cites this paper as Lein et al., 2007
In the citing paper
“Allen Brain Atlas in situ hybridization data [24] show ATF3 expression only in granular neurons of the olfactory bulb and dentate gyrus”
From Tamoxifen induces cellular stress in the nervous system by inhibiting cholesterol synthesis (2015) · cites this paper as [24]
In the citing paper
“Further in situ hybridization reveals that cerebellar Purkinje cells and neurons of the deep cerebellar nuclei express high levels of Clec16a (Allen Mouse Brain Atlas, http://mouse.brain-map.org/gene/show/50215)242526.”
From Clec16a is Critical for Autolysosome Function and Purkinje Cell Survival (2016) · cites this paper as [24]
In the citing paper
“we analyzed Nlk expression by LacZ staining and found that LacZ staining was strongest in the Purkinje cell layer (Fig.4D)”
From Polyglutamine Disease Toxicity Is Regulated by Nemo-like Kinase in Spinocerebellar Ataxia Type 1 (2013) · cites this paper as Lein et al., 2007
In the citing paper
“In animal studies (rodents and non-human primates), this is feasible through the use of comprehensive, histologically and functionally defined whole-brain areal parcellations (Bezgin et al., 2012; Lein et al., 2007; Paxinos et al., 2000; Saleem and Logothetis, 2007; Swanson, 2015; Van Essen et al., 2012).”
From Development of large-scale functional networks from birth to adulthood: A guide to the neuroimaging literature (2017) · cites this paper as Lein et al., 2007
In the citing paper
“ApoE expression, in both mice and humans, begins relatively late in development [46, 47].”
From ApoE, ApoE Receptors, and the Synapse in Alzheimer's Disease (2017) · cites this paper as [47]
In the citing paper
“To complement and validate the microarray data, several targeted, large-scale in situ hybridization (ISH) data sets were generated using a high-throughput ISH platform1, 8.”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [1]
In the citing paper
“In rodents, brain- and transcriptome-wide, cellular-resolution maps of transcript distributions are widely useful resources to complement genomic sequence data1, 2, 3.”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [1]
In the citing paper
“consistent with the percentage of genes expressed in mouse brain by ISH (80%; ref. 1) and fetal human brain by microarrays (76%; ref. 11).”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [1]
In the citing paper
“expression in human differs from that in mouse (Fig. 5d) and rhesus monkey (Fig. 5e), where CALB1 is robustly expressed in CA1 and CA2 in addition to dentate gyrus.”
From An anatomically comprehensive atlas of the adult human brain transcriptome (2012) · cites this paper as [1]
In the citing paper
“The atlas of the mid-gestational human brain described here, part of the BrainSpan Atlas of the Developing Human Brain, builds on digital molecular brain atlasing efforts in mouse20,22,24 and adult human23 by providing transcriptome resources on prenatal specimens typically inaccessible for research.”
From Transcriptional landscape of the prenatal human brain (2014) · cites this paper as [24]
In the citing paper
“These cell-type-specific expression patterns exhibited specific anatomical localization in the developing cerebellum (Fig. 1c) 26 .”
From Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells (2018) · cites this paper as [26]
In the citing paper
“The distribution of specific markers ( Pcp4 and Slc17a7 ) captured by Stereo-seq exhibited the expected similarity to in situ hybridization (ISH) data taken from Allen Brain Atlas (ABA) (Lein et al., 2007) and clearer patterns than HDST (Vickovic et al., 2019) or Slide-seqV2-resolved (Stickels et al., 2021) expression data (Figure S1E).”
From Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays (2022) · cites this paper as Lein et al., 2007
In the citing paper
“The expression patterns of Hes1 and Hes5 are consistent with ISH images taken from ABA (Figure S7H) (Lein et al., 2007).”
From Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays (2022) · cites this paper as Lein et al., 2007
In the citing paper
“These results are in line with ISH images of the Rspo1 and Fgf15 taken from ABA (Lein et al., 2007) (Figure S7F).”
From Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays (2022) · cites this paper as Lein et al., 2007
In the citing paper
“The expression patterns of Erbb4 and Gad2 are consistent with ISH images taken from ABA (Lein et al., 2007) (Figure S6F).”
From Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays (2022) · cites this paper as Lein et al., 2007
In the citing paper
“Finally, we compared all marker genes that we highlight in this paper (those in Table 1 and all figures) to their patterns in a recent spatial transcriptomics analysis of the spinal cord28 and to the Allen29 and Gensat30 expression databases and found general concordance between these resources (Supplementary Table 4).”
From A harmonized atlas of mouse spinal cord cell types and their spatial organization (2021) · cites this paper as [29]
In the citing paper
“Initial clustering identified 106,728 neurons, of which 70.2% were localized to BNST by examination of marker expression in the Allen Brain Atlas (ABA) (Lein et al., 2007) (Figure S3B).”
From Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity (2019) · cites this paper as Lein et al., 2007
In the citing paper
“In situ hybridization and microarray data, for example the Allen Brain Atlases (Hawrylycz et al., 2012; Lein et al., 2007), have also established that mRNA transcripts encoding these five NPPs and that many other NPPs and NP-GPCR genes are expressed differentially in many brain regions.”
From Single-cell transcriptomic evidence for dense intracortical neuropeptide networks (2019) · cites this paper as Lein et al., 2007
In the citing paper
“Inspection of ISHs from the Allen Brain Atlas (Lein et al., 2007) indicated that these neurons were located in the Edinger-Westphal nucleus, which is adjacent to the DRN, confirming that our dissection region spanned most of the DRN along the anterior-posterior axis.”
From Molecular and anatomical organization of the dorsal raphe nucleus (2019) · cites this paper as Lein et al., 2007
In the citing paper
“We leveraged the inclusion of adjacent brain tissue in our atlas to map the boundary between the 3V ChP and developing pineal gland using published ISH (Lein et al., 2007; Visel et al., 2004) of marker genes from our data (Figure S2C).”
From A cellular and spatial map of the choroid plexus across brain ventricles and ages (2021) · cites this paper as Lein et al., 2007
In the citing paper
“Signature scores were distinctly elevated in areas corresponding to the anatomical structures annotated in the Allen brain reference atlas (Figure S3A) (Lein et al., 2007).”
From Atlas of the aging mouse brain reveals white matter as vulnerable foci (2023) · cites this paper as Lein et al., 2007
In the citing paper
“We compared the expression of marker genes to insitu hybridization (ISH) data from the Allen Mouse Brain Atlas(Lein et al., 2007) and visual landmarks from the H&E microscopy images”
From Atlas of the aging mouse brain reveals white matter as vulnerable foci (2023) · cites this paper as Lein et al., 2007
Citations
Cites
DAVID: Database for Annotation, Visualization, and Integrated Discovery
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327
The Transcriptional Landscape of the Mammalian Genome
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492
Interneurons of the neocortical inhibitory system
Markram, H., Toledo-Rodriguez, M., Wang, Y., Gupta, A., Silberberg, G., & Wu, C. (2004) · Nature Reviews Neuroscience · doi:10.1038/nrn1519 · Cited by 2,954
Alignment by Maximization of Mutual Information
Viola, P. A., & Wells, W. M. (1997) · International Journal of Computer Vision · doi:10.1023/a:1007958904918 · Cited by 2,610
Coordinated Transcription of Key Pathways in the Mouse by the Circadian Clock
Panda, S., Antoch, M. P., Miller, B. H., Su, A. I., Schook, A. C., Straume, M., Schultz, P. G., Kay, S. A., Takahashi, J. S., & Hogenesch, J. B. (2002) · Cell · doi:10.1016/s0092-8674(02)00722-5 · Cited by 2,310
The three-dimensional organization of the hippocampal formation: A review of anatomical data
Amaral, D. G., & Witter, M. P. (1989) · Neuroscience · doi:10.1016/0306-4522(89)90424-7 · Cited by 2,180
A gene expression atlas of the central nervous system based on bacterial artificial chromosomes
Gong, S., Zheng, C., Doughty, M. L., Losos, K., Didkovsky, N., Schambra, U. B., Nowak, N. J., Joyner, A., Leblanc, G., Hatten, M. E., et al. (2003) · Nature · doi:10.1038/nature02033 · Cited by 2,108
Zola-Morgan, S., Squire, L., & Amaral, D. (1986) · The Journal of Neuroscience · doi:10.1523/jneurosci.06-10-02950.1986 · Cited by 1,997
de Nó, R. L. (1934) · Cited by 1,974
Brain Maps: Structure of the Rat Brain
Swanson, L. W. (1992) · Medical Entomology and Zoology · Cited by 1,878
Flagged first, then by citations
1 of the 58 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- 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)
Cited by
Sorted by citations
Items 501–600 of 1,058
Single-cell transcriptomic evidence for dense intracortical neuropeptide networks
Smith, S. J., Sümbül, U., Graybuck, L. T., Collman, F., Seshamani, S., Gala, R., Gliko, O., Elabbady, L., Miller, J. A., Bakken, T. E., et al. (2019) · eLife · doi:10.7554/elife.47889 · Cited by 156
Self-citationPolyzos, A. A., Lee, D. Y., Datta, R., Hauser, M., Budworth, H., Holt, A., Mihalik, S. J., Goldschmidt, P., Frankel, K. A., Trego, K. S., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.03.004 · Cited by 152
Kozlenkov, A., Roussos, P., Timashpolsky, A., Barbu, M., Rudchenko, S., Bibikova, M. V., Klotzle, B., Byne, W. M., Lyddon, R., Narzo, A. F. D., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt838 · Cited by 159
Smith, C. M., Shen, P., Banerjee, A., Bonaventure, P., Ma, S., Bathgate, R. A. D., Sutton, S. W., & Gundlach, A. L. (2010) · The Journal of Comparative Neurology · doi:10.1002/cne.22442 · Cited by 156
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.
Chen, A., Liao, S., Cheng, M., Ma, K., Wu, L. L., Lai, Y., Qiu, X., Yang, J., Xu, J., Hao, S., et al. (2022) · Apollo (University of Cambridge) · Cited by 154
Self-citationBrainstem neurons that command mammalian locomotor asymmetries
Cregg, J. M., Leiras, R., Montalant, A., Wanken, P., Wickersham, I. R., & Kiehn, O. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0633-7 · Cited by 154
Gradients in the Brain: The Control of the Development of Form and Function in the Cerebral Cortex
Sansom, S. N., & Livesey, F. J. (2009) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a002519 · Cited by 148
Kurrasch, D. M., Cheung, C. C., Lee, F. Y., Tran, P. V., Hata, K., & Ingraham, H. A. (2007) · Journal of Neuroscience · doi:10.1523/jneurosci.2858-07.2007 · Cited by 157
A Central Extended Amygdala Circuit That Modulates Anxiety
Ahrens, S., Wu, M. V., Furlan, A., Hwang, G., Paik, R., Li, H., Penzo, M. A., Tollkühn, J., & Li, B. (2018) · Journal of Neuroscience · doi:10.1523/jneurosci.0705-18.2018 · Cited by 157
Histology-derived volumetric annotation of the human hippocampal subfields in postmortem MRI
Adler, D. H., Pluta, J. B., Kadivar, S., Craige, C. P., Gee, J. C., Avants, B., & Yushkevich, P. A. (2013) · NeuroImage · doi:10.1016/j.neuroimage.2013.08.067 · Cited by 155
Elfn1 Regulates Target-Specific Release Probability at CA1-Interneuron Synapses
Sylwestrak, E. L., & Ghosh, A. (2012) · Science · doi:10.1126/science.1222482 · Cited by 151
Reward Inhibits Paraventricular CRH Neurons to Relieve Stress
Yuan, Y., Wu, W., Chen, M., Cai, F., Fan, C., Shen, W., Sun, W., & Hu, J. (2019) · Current Biology · doi:10.1016/j.cub.2019.02.048 · Cited by 151
Bao, H., Asrican, B., Li, W., Gu, B., Wen, Z., Lim, S.-A., Haniff, I., Ramakrishnan, C., Deisseroth, K., Philpot, B., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.10.003 · Cited by 151
A comprehensive thalamocortical projection map at the mesoscopic level
Hunnicutt, B. J., Long, B., Kusefoglu, D., Gertz, K. J., Zhong, H., & Mao, T. (2014) · Nature Neuroscience · doi:10.1038/nn.3780 · Cited by 156
Mirabella, F., Desiato, G., Mancinelli, S., Fossati, G., Rasile, M., Morini, R., Markicevic, M., Grimm, C., Amegandjin, C. A., Termanini, A., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.10.006 · Cited by 152
The adhesion GPCR Gpr56 regulates oligodendrocyte development via interactions with Gα12/13 and RhoA
Ackerman, S. D., Garcia, C. M., Piao, X., Gutmann, D. H., & Monk, K. R. (2015) · Nature Communications · doi:10.1038/ncomms7122 · Cited by 149
RNAs as extracellular signaling molecules
Dinger, M. E., Mercer, T. R., & Mattick, J. S. (2008) · Journal of Molecular Endocrinology · doi:10.1677/jme-07-0160 · Cited by 148
RNA editing, DNA recoding and the evolution of human cognition
Mattick, J. S., & Mehler, M. F. (2008) · Trends in Neurosciences · doi:10.1016/j.tins.2008.02.003 · Cited by 148
Discovery of rare cells from voluminous single cell expression data
Jindal, A., Gupta, P., Jayadeva, & Sengupta, D. (2018) · Nature Communications · doi:10.1038/s41467-018-07234-6 · Cited by 148
BrainAligner: 3D registration atlases of Drosophila brains
Peng, H., Chung, P., Long, F., Qu, L., Jenett, A., Seeds, A. M., Myers, E. W., & Simpson, J. H. (2011) · Nature Methods · doi:10.1038/nmeth.1602 · Cited by 147
Shah, S., Lubeck, E., Zhou, W., & Cai, L. (2017) · Neuron · doi:10.1016/j.neuron.2017.05.008 · Cited by 147
Cannabinoid CB2 receptors in the mouse brain: relevance for Alzheimer’s disease
López, A., Aparicio, N., Pazos, M. R., Grande, M. T., Barreda-Manso, M. A., Benito‐Cuesta, I., Vázquez, C., Amores, M., Ruiz‐Pérez, G., García-García, E., et al. (2018) · Journal of Neuroinflammation · doi:10.1186/s12974-018-1174-9 · Cited by 151
Beyond reward prediction errors: the role of dopamine in movement kinematics
Barter, J. W., Li, S., Lu, D., Bartholomew, R. A., Rossi, M. A., Shoemaker, C. T., Salas-Meza, D., Gaidis, E., & Yin, H. H. (2015) · Frontiers in Integrative Neuroscience · doi:10.3389/fnint.2015.00039 · Cited by 146
The Human Language–Associated Gene SRPX2 Regulates Synapse Formation and Vocalization in Mice
Sia, G.-M., Clem, R. L., & Huganir, R. L. (2013) · Science · doi:10.1126/science.1245079 · Cited by 153
Wisor, J. P., Pasumarthi, R. K., Gerashchenko, D., Thompson, C. L., Pathak, D. S., Sancar, A., Franken, P., Lein, E. S., & Kilduff, T. S. (2008) · Journal of Neuroscience · doi:10.1523/jneurosci.1150-08.2008 · Cited by 145
Self-citationWong, T. T. W., Zhang, R., Zhang, C., Hsu, H., Maslov, K., Wang, L., Shi, J., Chen, R., Shung, K. K., Zhou, Q., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01649-3 · Cited by 146
Laser Ablation–Inductively Coupled Plasma–Mass Spectrometry Imaging in Biology
Doble, P., de Vega, R. G., Bishop, D., Hare, D. J., & Clases, D. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c01219 · Cited by 153
Jessa, S., Mohammadnia, A., Harutyunyan, A. S., Hulswit, M., Varadharajan, S., Lakkis, H., Kabir, N., Bashardanesh, Z., Hébert, S., Faury, D., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01205-w · Cited by 150
Wan, X., Xiao, J., Tam, S. S. T., Cai, M., Sugimura, R., Wang, Y., Wan, X., Lin, Z., Wu, A. R., & Yang, C. (2023) · Nature Communications · doi:10.1038/s41467-023-43629-w · Cited by 166
Stress‐induced dynamic routing of hippocampal connectivity: A hypothesis
Segal, M., Richter‐Levin, G., & Maggio, N. (2010) · Hippocampus · doi:10.1002/hipo.20751 · Cited by 146
Cerebellar associative sensory learning defects in five mouse autism models
Kloth, A. D., Badura, A., Li, A., Cherskov, A., Connolly, S. G., Giovannucci, A., Bangash, M. A., Grasselli, G., Peñagarikano, O., Piochon, C., et al. (2015) · eLife · doi:10.7554/elife.06085 · Cited by 148
Durand, S., Iyer, R., Mizuseki, K., de Vries, S. E. J., Mihalaş, Ş., & Reid, R. C. (2016) · Journal of Neuroscience · doi:10.1523/jneurosci.1741-16.2016 · Cited by 146
Jensen, C. B., Pyke, C., Rasch, M. G., Dahl, A. B., Knudsen, L. B., & Secher, A. (2018) · Endocrinology · doi:10.1210/en.2017-00812 · Cited by 145
Kim, C. K., Ye, L., Jennings, J. H., Pichamoorthy, N., Tang, D. D., Yoo, A.-C. W., Ramakrishnan, C., & Deisseroth, K. (2017) · Cell · doi:10.1016/j.cell.2017.07.020 · Cited by 145
Gene-Network Analysis Identifies Susceptibility Genes Related to Glycobiology in Autism
van der Zwaag, B., Franke, L., Poot, M., Hochstenbach, R., Spierenburg, H. A., Vorstman, J. A. S., van Daalen, E., de Jonge, M. V., Verbeek, N. E., Brilstra, E. H., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005324 · Cited by 147
Interaction between autism-linked MDGAs and neuroligins suppresses inhibitory synapse development
Pettem, K. L., Yokomaku, D., Takahashi, H., Ge, Y., & Craig, A. M. (2013) · The Journal of Cell Biology · doi:10.1083/jcb.201206028 · Cited by 150
Wnt signaling in Alzheimer's disease: Up or down, that is the question
Boonen, R. A. C. M., van Tijn, P., & Živković, D. (2008) · Ageing Research Reviews · doi:10.1016/j.arr.2008.11.003 · Cited by 143
Mitochondrial Dysfunction and Immune Activation are Detectable in Early Alzheimer's Disease Blood
Lunnon, K., Ibrahim, Z. M., Proitsi, P., Lourdusamy, A., Newhouse, S., Sattlecker, M., Furney, S. J., Saleem, M., Soininen, H. S., Kłoszewska, I., et al. (2012) · Journal of Alzheimer s Disease · doi:10.3233/jad-2012-111592 · Cited by 145
Brain size and limits to adult neurogenesis
Paredes, M. F., Sorrells, S. F., García‐Verdugo, J. M., & Álvarez-Buylla, A. (2015) · The Journal of Comparative Neurology · doi:10.1002/cne.23896 · Cited by 148
The Effect of Acute and Chronic Social Stress on the Hippocampal Transcriptome in Mice
Stankiewicz, A. M., Gościk, J., Majewska, A., Swiergiel, A. H., & Juszczak, G. R. (2015) · PLoS ONE · doi:10.1371/journal.pone.0142195 · Cited by 145
Pryce, C. R. (2007) · Brain Research Reviews · doi:10.1016/j.brainresrev.2007.08.005 · Cited by 147
Morgan, J. L., & Lichtman, J. W. (2013) · Nature Methods · doi:10.1038/nmeth.2480 · Cited by 150
Self-citationStress and Anxiety Across the Lifespan: Structural Plasticity and Epigenetic Regulation
Hunter, R. G., & McEwen, B. S. (2013) · Epigenomics · doi:10.2217/epi.13.8 · Cited by 142
DNA methylation map of mouse and human brain identifies target genes in Alzheimer’s disease
Sanchez-Mut, J. V., Aso, E., Panayotis, N., Lott, I., Dierssen, M., Rabano, A., Urdinguio, R. G., Fernandez, A. F., Astudillo, A., Martin-Subero, J. I., et al. (2013) · Brain · doi:10.1093/brain/awt237 · Cited by 144
Autism gene Ube3a and seizures impair sociability by repressing VTA Cbln1
Krishnan, V., Stoppel, D. C., Nong, Y., Johnson, M. A., Nadler, M. J. S., Özkaynak, E., Teng, B. L., Nagakura, I., Mohammad, F., Silva, M. A., et al. (2017) · Nature · doi:10.1038/nature21678 · Cited by 142
Bmal1 function in skeletal muscle regulates sleep
Ehlen, J. C., Brager, A. J., Baggs, J. E., Pinckney, L., Gray, C. L., DeBruyne, J. P., Esser, K. A., Takahashi, J. S., & Paul, K. N. (2017) · eLife · doi:10.7554/elife.26557 · Cited by 150
Jones, E. V., Bernardinelli, Y., Tse, Y. C., Chierzi, S., Wong, T. P., & Murai, K. K. (2011) · Journal of Neuroscience · doi:10.1523/jneurosci.4757-10.2011 · Cited by 145
Phelan, K. D., Shwe, U. T., Abramowitz, J., Wu, H., Rhee, S. W., Howell, M. D., Gottschall, P. E., Freichel, M., Flockerzi, V., Birnbaumer, L., et al. (2012) · Molecular Pharmacology · doi:10.1124/mol.112.082271 · Cited by 143
Self-citationComprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques
He, Z., Han, D., Efimova, O., Guijarro, P., Yu, Q., Oleksiak, A., Jiang, S., Anokhin, K. V., Velichkovsky, B. M., Grünewald, S., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4548 · Cited by 137
Molecular Profiling of Neurons Based on Connectivity
Ekstrand, M. I., Nectow, A. R., Knight, Z. A., Latcha, K. N., Pomeranz, L. E., & Friedman, J. M. (2014) · Cell · doi:10.1016/j.cell.2014.03.059 · Cited by 143
Todd, W. D., Venner, A., Anaclet, C., Broadhurst, R. Y., Luca, R. D., Bandaru, S. S., Issokson, L., Hablitz, L. M., Cravetchi, O., Arrigoni, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17197-2 · Cited by 145
Li, F., Sami, A., Noristani, H. N., Slattery, K., Qiu, J., Groves, T., Wang, S., Veerasammy, K., Chen, Y. X., Morales, J., et al. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.08.015 · Cited by 147
A genuine layer 4 in motor cortex with prototypical synaptic circuit connectivity
Yamawaki, N., Borges, K., Suter, B. A., Harris, K. D., & Shepherd, G. M. G. (2014) · eLife · doi:10.7554/elife.05422 · Cited by 141
Tzingounis, A. V., Heidenreich, M., Kharkovets, T., Spitzmaul, G. F., Jensen, H. S., Nicoll, R. A., & Jentsch, T. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004644107 · Cited by 141
Quantified Coexpression Analysis of Central Amygdala Subpopulations
McCullough, K. M., Morrison, F. G., Hartmann, J., Carlezon, W. A., & Ressler, K. J. (2018) · eNeuro · doi:10.1523/eneuro.0010-18.2018 · Cited by 149
Kato, A., Zhou, W., Milstein, A. D., Knierman, M. D., Siuda, E. R., Dotzlaf, J. E., Yu, H. Y., Hale, J. E., Nisenbaum, E. S., Nicoll, R. A., et al. (2007) · Journal of Neuroscience · doi:10.1523/jneurosci.5561-06.2007 · Cited by 144
A non-circadian role for clock-genes in sleep homeostasis:a strain comparison
Franken, P., Thomason, R. G., Heller, H. C., & O’Hara, B. F. (2007) · BMC Neuroscience · doi:10.1186/1471-2202-8-87 · Cited by 141
Han, B., Zhou, S., Zhang, Y., Chen, S., Xi, W., Liu, C., Zhou, X., Yuan, M., Yu, X., Li, L., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.adg1323 · Cited by 143
Reversal of Depressed Behaviors in Mice by p11 Gene Therapy in the Nucleus Accumbens
Alexander, B., Warner-Schmidt, J., Eriksson, T. M., Tamminga, C., Arango-Lievano, M., Ghose, S., Vernov, M., Stavarache, M., Musatov, S., Flajolet, M., et al. (2010) · Science Translational Medicine · doi:10.1126/scitranslmed.3001079 · Cited by 140
Genomic approach to selective vulnerability of the hippocampus in brain ischemia–hypoxia
Schmidt‐Kastner, R. (2015) · Neuroscience · doi:10.1016/j.neuroscience.2015.08.034 · Cited by 139
Contributions of 5-HT neurons to respiratory control: Neuromodulatory and trophic effects
Hodges, M. R., & Richerson, G. B. (2008) · Respiratory Physiology & Neurobiology · doi:10.1016/j.resp.2008.05.014 · Cited by 140
Contribution of KCNQ2 and KCNQ3 to the medium and slow afterhyperpolarization currents
Tzingounis, A. V., & Nicoll, R. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810535105 · Cited by 138
Neuropeptide and small transmitter coexistence: Fundamental studies and relevance to mental illness
Hökfelt, T., Barde, S., Xu, Z.-Q. D., Kuteeva, E., Rüegg, J., Le Maitre, E., Risling, M., Kehr, J., Ihnatko, R., Theodorsson, E., et al. (2018) · Frontiers in Neural Circuits · doi:10.3389/fncir.2018.00106 · Cited by 139
Wallis, K., Dudazy-Gralla, S., van Hogerlinden, M., Nordström, K., Mittag, J., & Vennström, B. (2010) · Molecular Endocrinology · doi:10.1210/me.2010-0175 · Cited by 143
Molecular Genetics of Addiction and Related Heritable Phenotypes
Uhl, G. R., Drgon, T., Johnson, C., Li, C., Contoreggi, C. S., Hess, J., Naiman, D. Q., & Liu, Q. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1441.018 · Cited by 141
ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains
Ronneberger, O., Liu, K., Rath, M., Rueβ, D., Mueller, T., Skibbe, H., Drayer, B., Schmidt, T., Filippi, A., Nitschke, R., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2076 · Cited by 138
Mapping gene regulatory circuitry of Pax6 during neurogenesis
Thakurela, S., Tiwari, N., Schick, S., Garding, A., Ivánek, R., Berninger, B., & Tiwari, V. K. (2016) · Cell Discovery · doi:10.1038/celldisc.2015.45 · Cited by 136
A Neuron-Optimized CRISPR/dCas9 Activation System for Robust and Specific Gene Regulation
Savell, K. E., Bach, S. V., Zipperly, M. E., Revanna, J. S., Goska, N. A., Tuscher, J. J., Duke, C. G., Sultan, F. A., Burke, J. N., Williams, D., et al. (2019) · eNeuro · doi:10.1523/eneuro.0495-18.2019 · Cited by 137
A Spatiomolecular Map of the Striatum
Märtin, A., Calvigioni, D., Tzortzi, O., Fuzik, J., Wärnberg, E., & Meletis, K. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.096 · Cited by 132
From whole-mount to single-cell spatial assessment of gene expression in 3D
Waylen, L. N., Nim, H. T., Martelotto, L. G., & Ramialison, M. (2020) · Communications Biology · doi:10.1038/s42003-020-01341-1 · Cited by 137
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGEPreprint
Valen, E., Pascarella, G., Chalk, A. M., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarević, D., Motti, D., et al. (2008) · Genome Research · doi:10.1101/gr.084541.108 · Cited by 140
Lozovaya, N., Eftekhari, S., Cloarec, R., Gouty‐Colomer, L., Dufour, A., Riffault, B., Billon-Grand, M., Pons-Bennaceur, A., Oumar, N., Burnashev, N., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03802-y · Cited by 143
Moran, S. P., Maksymetz, J., & Conn, P. J. (2019) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2019.10.007 · Cited by 137
Paquelet, G. E., Carrion, K., Lacefield, C., Zhou, P., Hen, R., & Miller, B. R. (2022) · Neuron · doi:10.1016/j.neuron.2022.05.015 · Cited by 139
FoxO6 regulates memory consolidation and synaptic functionPreprint
Salih, D. A. M., Rashid, A. J., Colas, D., de la Torre-Ubieta, L., Zhu, R. P., Morgan, A. A., Santo, E. E., Ucar, D., Devarajan, K., Cole, C. J., et al. (2012) · Genes & Development · doi:10.1101/gad.208926.112 · Cited by 136
A neuronal hub binding sleep initiation and body cooling in response to a warm external stimulus
Harding, E. C., Yu, X., Miao, A., Andrews, N., Ma, Y., Ye, Z., Lignos, L., Miracca, G., Ba, W., Yustos, R., et al. (2018) · Current Biology · doi:10.1016/j.cub.2018.05.054 · Cited by 136
Gibrat, C., Saint‐Pierre, M., Bousquet, M., Lévesque, D., Rouillard, C., & Cicchetti, F. (2009) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2009.06072.x · Cited by 136
The medial habenula: still neglected
Viswanath, H., Carter, A. Q., Baldwin, P. R., Molfese, D. L., & Salas, R. (2014) · Frontiers in Human Neuroscience · doi:10.3389/fnhum.2013.00931 · Cited by 142
James, S., Churches, Q. I., de Jonge, M. D., Birchall, I. E., Streltsov, V. A., McColl, G., Adlard, P. A., & Hare, D. J. (2016) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.6b00362 · Cited by 136
AMPA receptor structure and auxiliary subunits
Kamalova, A., & Nakagawa, T. (2020) · The Journal of Physiology · doi:10.1113/jp278701 · Cited by 139
9-cis-13,14-Dihydroretinoic Acid Is an Endogenous Retinoid Acting as RXR Ligand in Mice
Rühl, R., Krzyżosiak, A., Niewiadomska-Cimicka, A., Rochel, N., Széles, L., Vaz, B., Wietrzych, M., Álvarez, S., Szklenár, M., Nagy, L., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005213 · Cited by 136
Chumley, M. J., Catchpole, T., Silvany, R. E., Kernie, S. G., & Henkemeyer, M. J. (2007) · Journal of Neuroscience · doi:10.1523/jneurosci.4158-07.2007 · Cited by 136
Mallach, A., Zielonka, M., van Lieshout, V., An, Y., Khoo, J. H., Vanheusden, M., Chen, W.-T., Moechars, D., Arancibia-Carcamo, I. L., Fiers, M., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114216 · Cited by 135
Park, D. H., Hong, S. J., Salinas, R. D., Liu, S. J., Sun, S. W., Sgualdino, J., Testa, G., Matzuk, M. M., Iwamori, N., & Lim, D. A. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.060 · Cited by 139
Visualizing anatomically registered data with brainrender
Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T. W., Portugues, R., & Branco, T. (2021) · eLife · doi:10.7554/elife.65751 · Cited by 136
A molecular switch for neuroprotective astrocyte reactivity
Cameron, E. G., Nahmou, M. M., Toth, A. B., Heo, L., Tanasă, B., Dalal, R., Yan, W., Nallagatla, P., Xia, X., Hay, S., et al. (2023) · Nature · doi:10.1038/s41586-023-06935-3 · Cited by 137
Social trauma engages lateral septum circuitry to occlude social reward
Li, L., Durand-de Cuttoli, R., Aubry, A. V., Burnett, C. J., Cathomas, F., Parise, L. F., Chan, K. L., Morel, C., Yuan, C., Shimo, Y., et al. (2023) · Nature · doi:10.1038/s41586-022-05484-5 · Cited by 134
Neuropathological and transcriptomic characteristics of the aged brain
Miller, J. A., Guillozet-Bongaarts, A., Gibbons, L. E., Postupna, N., Renz, A., Beller, A. E., Sunkin, S. M., Ng, L., Rose, S. E., Smith, K. A., et al. (2017) · eLife · doi:10.7554/elife.31126 · Cited by 134
Self-citationTARP Auxiliary Subunits Switch AMPA Receptor Antagonists into Partial Agonists
Menuz, K., Stroud, R. M., Nicoll, R. A., & Hays, F. A. (2007) · Science · doi:10.1126/science.1146317 · Cited by 136
Xu, X., Li, C., Gao, X., Xia, K., Guo, H., Li, Y., Hao, Z., Zhang, L., Gao, D., Xu, C., et al. (2017) · Cell Research · doi:10.1038/cr.2017.132 · Cited by 132
Gorinski, N., Bijata, M., Prasad, S., Wirth, A., Galil, D. A., Zeug, A., Базовкина, Д. В., Kondaurova, E. M., Kulikova, E. A., Ilchibaeva, T. V., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11876-5 · Cited by 135
Simons, S. B., Escobedo, Y., Yasuda, R., & Dudek, S. M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904775106 · Cited by 134
The Fowler Syndrome-Associated Protein FLVCR2 Is an Importer of Heme
Duffy, S. P., Shing, J. C., Saraon, P., Berger, L., Eiden, M. V., Wilde, A., & Tailor, C. S. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.00690-10 · Cited by 136
Aneuploidy: From a Physiological Mechanism of Variance to Down Syndrome
Dierssen, M., Hérault, Y., & Estivill, X. (2009) · Physiological Reviews · doi:10.1152/physrev.00032.2007 · Cited by 143
Wu, S., Joseph, A., Hammonds, A. S., Celniker, S., Yu, B., & Frise, E. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521171113 · Cited by 128
Behavioral Strategy Determines Frontal or Posterior Location of Short-Term Memory in Neocortex
Gilad, A., Gallero-Salas, Y., Groos, D., & Helmchen, F. (2018) · Neuron · doi:10.1016/j.neuron.2018.07.029 · Cited by 140
A neural circuit mechanism for mechanosensory feedback control of ingestion
Kim, D.-Y., Heo, G., Kim, M., Kim, H., Jin, J. A., Kim, H. K., Jung, S., An, M., Ahn, B. H., Park, J. H., et al. (2020) · Nature · doi:10.1038/s41586-020-2167-2 · Cited by 133
Phasic Activation of Dorsal Raphe Serotonergic Neurons Increases Pupil Size
Cazettes, F., Reato, D., Morais, J. P., Renart, A., & Mainen, Z. F. (2020) · Current Biology · doi:10.1016/j.cub.2020.09.090 · Cited by 146
Cortical thickness measured from MRI in the YAC128 mouse model of Huntington's disease
Lerch, J. P., Carroll, J. B., Dorr, A. E., Spring, S., Evans, A. C., Hayden, M. R., Sled, J. G., & Henkelman, R. M. (2008) · NeuroImage · doi:10.1016/j.neuroimage.2008.02.019 · Cited by 134
Hofstetter, A. O., Saha, S., Siljehav, V., Jakobsson, P., & Herlenius, E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611468104 · Cited by 133
Metadata
- Authors
- Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., Chen, L., Chen, L., Chen, T.-M., Chi Chin, M., Chong, J., Crook, B. E., Czaplinska, A., Dang, C. N., Datta, S., Dee, N. R., Desaki, A. L., Desta, T., Diep, E., Dolbeare, T. A., Donelan, M. J., Dong, H.-W., Dougherty, J. G., Duncan, B. J., Ebbert, A. J., Eichele, G., Estin, L. K., Faber, C., Facer, B. A., Fields, R., Fischer, S. R., Fliss, T. P., Frensley, C., Gates, S. N., Glattfelder, K. J., Halverson, K. R., Hart, M. R., Hohmann, J. G., Howell, M. P., Jeung, D. P., Johnson, R. A., Karr, P. T., Kawal, R., Kidney, J. M., Knapik, R. H., Kuan, C. L., Lake, J. H., Laramee, A. R., Larsen, K. D., Lau, C., Lemon, T. A., Liang, A. J., Liu, Y., Luong, L. T., Michaels, J., Morgan, J. J., Morgan, R. J., Mortrud, M. T., Mosqueda, N. F., Ng, L. L., Ng, R., Orta, G. J., Overly, C. C., Pak, T. H., Parry, S. E., Pathak, S. D., Pearson, O. C., Puchalski, R. B., Riley, Z. L., Rockett, H. R., Rowland, S. A., Royall, J. J., Ruiz, M. J., Sarno, N. R., Schaffnit, K., Shapovalova, N. V., Sivisay, T., Slaughterbeck, C. R., Smith, S. C., Smith, K. A., Smith, B. I., Sodt, A. J., Stewart, N. N., Stumpf, K.-R., Sunkin, S. M., Sutram, M., Tam, A., Teemer, C. D., Thaller, C., Thompson, C. L., Varnam, L. R., Visel, A., Whitlock, R. M., Wohnoutka, P. E., Wolkey, C. K., Wong, V. Y., Wood, M., Yaylaoglu, M. B., Young, R. C., Youngstrom, B. L., Feng Yuan, X., Zhang, B., Zwingman, T. A., & Jones, A. R.
- Affiliations
- Allen Institute for Brain Science (US)
- Baylor College of Medicine (US)
- Novartis (Switzerland) (CH)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Lein, Ed S.
- Jones, Allan R.
- ORCID
- Lein, Ed S.
- Hawrylycz, Michael J.
- Bernard, Amy
- Chen, Lin
- Chong, Jimmy
- Dee, Nick R.
- Desta, Tsega
- Dolbeare, Tim A.
- Dong, Hong-Wei
- Fliss, Tim P.
- Glattfelder, Katie J.
- Hart, Matthew R.
- Hohmann, John G.
- Liu, Ying
- Ng, Lydia L.
- Puchalski, Ralph B.
- Shapovalova, Nadiya V.
- Smith, Kimberly A.
- Sunkin, Susan M.
- Thompson, Carol L.
- Visel, Axel
- Wohnoutka, Paul E.
- Wood, Matthew
- Zhang, Bin
- Zwingman, Theresa A.
- Jones, Allan R.
- Venue
- Nature
- Published
- 2006-12-06
- Volume
- 445
- Issue
- 7124
- Pages
- 168-176
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2123491442
- Cited by
- 5,572
- References
- 58
- Citations by year
- 2026: 237 · 2025: 327 · 2024: 368 · 2023: 347 · 2022: 409 · 2021: 435 · 2020: 398 · 2019: 342 · 2018: 320 · 2017: 296 · 2016: 280 · 2015: 236 · 2014: 252 · 2013: 203 · 2012: 223
- FWCI
- 68.18
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- gene expression atlas, mouse brain, Allen Brain Atlas, cellular resolution, in situ hybridization, brain region-specific gene expression, cell markers, brain organization
- MeSH terms
- Animals, Brain, Gene Expression Regulation, Hippocampus, Male, Mice, Inbred C57BL, Organ Specificity, RNA, Messenger, Genome, Computational Biology, Gene Expression Profiling, Genomics, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
