A digital atlas to characterize the mouse brain transcriptome

PLoS Computational Biology

Volumn 1, Issue 4, 2005, Pages 0289-0296

  Carson, James P ^a   Ju, Tao ^b   Lu, Hui Chen ^a   Thaller, Christina ^a   Xu, Mei ^c   Pallas, Sarah L ^c   Crair, Michael C ^a   Warren, Joe ^b   Chiu, Wah ^a   Eichele, Gregor ^d  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b Rice University   (United States)

^c GEORGIA STATE UNIVERSITY   (United States)

^d MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION;

CANDIDATE GENES; CELLULAR RESOLUTION; DOPAMINE TRANSPORTERS; FRAMES OF REFERENCE; GENE EXPRESSION PATTERNS; MOUSE BRAIN; PARKINSON'S DISEASE; SUBSTANTIA NIGRA; TRANSCRIPTOMES; USER QUERY;

MAMMALS;

ANATOMY; ANIMAL; ARTICLE; BIOLOGY; BRAIN; COMPUTER SIMULATION; FACTUAL DATABASE; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; IN SITU HYBRIDIZATION; MEDICAL ILLUSTRATION; METABOLISM; MOUSE;

ANATOMY, ARTISTIC; ANIMALS; BRAIN; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, FACTUAL; GENE EXPRESSION PROFILING; IN SITU HYBRIDIZATION; MEDICAL ILLUSTRATION; MICE; TRANSCRIPTION, GENETIC;

EID: 55449133888     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010041     Document Type: Article

References (39)

1. Neidhardt L, Gasca S, Wertz K, Obermayr F, Worpenberg S, et al. (2000) Large-scale screen for genes controlling mammalian embryo genes is, using high-throughput gene expression analysis in mouse embryos. Mech Dev 98: 77-94.
2. Visel A, Thaller C, Eichele G (2004) GenePaint.org: An atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res 32: D552-D556.
3. Boguski MS, Jones AR (2004) Neurogenomics: At the intersection of neurobiology and genome sciences. Nat Neurosci 7: 429-433.
4. Gray PA, Fu H, Luo P, Zhao Q, Yu J, et al. (2004) Mouse brain organization revealed through direct genome-scale TF expression analysis. Science 306: 2255-2257.
5. Gong S, Zheng C, Doughty ML, Losos K, Didkovsky N, et al. (2003) A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425: 917-925.
6. Hill DP, Begley DA, Finger JH, Hayamizu TF, McCright IJ, et al. (2004) The mouse Gene Expression Database (GXD): Updates and enhancements. Nucleic Acids Res 32: D568-D571.
7. Baldock RA, Bard JB, Burger A, Burton N, Christiansen J, et al. (2003) EMAP and EMAGE: A framework for understanding spatially organized data. Neuroinformatics 1: 309-325.
8. Brune RM, Bard JB, Dubreuil C, Guest E, Hill W, et al. (1999) A three-dimensional model of the mouse at embryonic day 9. Dev Biol 216: 457-468.
9. Carson JP, Thaller C, Eichele G (2002) A transcriptome atlas of the mouse brain at cellular resolution. Curr Opin Neurobiol 12: 562-565.
10. Valverde F (1998) Golgi atlas of the postnatal mouse brain. New York: Springer-Verlag. 146 p.
11. Ju T, Warren J, Eichele G, Thaller C, Chiu W, et al. (2003) A geometric database for gene expression data. In: Kobbelt L, Schröder P, Hoppe H, editors. Geometry processing 2003. Aachen (Germany): Eurographics Association, pp. 166-176
12. Carson JP, Eichele G, Chiu W (2005) A method for automated detection of gene expression required for the establishment of a digital transcriptomewide gene expression atlas. J Microsc 217: 275-281.
13. Fukuchi-Shimogori T, Grove EA (2001) Neocortex patterning by the secreted signaling molecule FGF8. Science 294: 1071-1074.
14. Woolsey TA, Van der Loos H (1970) The structural organization of layer IV in the somatosensory region of mouse cerebral cortex: The description of a cortical field composed of discrete cytoarchitectonic units. Brain Res 17: 205-242.
15. Abdel-Majid RM, Leong WL, Schalkwyk LC, Smallman DS, Wong ST, et al. (1998) Loss of adenylyl cyclase I activity disrupts patterning of mouse somatosensory cortex. Nat Genet 19: 289-291.
16. Heintz N (2004) Gene expression nervous system atlas (GENSAT). Nat Neurosci 7: 483.
17. Lein ES, Zhao X, Gage FH (2004) Defining a molecular atlas of the hippocampus using DNA microarrays and high-throughput in situ hybridization. J Neurosci 24: 3879-3889.
18. Sadowski M, Tang CY, Aguinaldo JG, Carp R, Meeker HC, et al. (2003) In vivo micro magnetic resonance imaging signal changes in scrapie infected mice. Neurosci Lett 345: 1-4.
19. Barlow C, Lockhart DJ (2002) DNA arrays and neurobiology - What's new and what's next? Curr Opin Neurobiol 12: 554-561.
20. Carson JP, Ju T, Thaller C, Warren J, Bello M, et al. (2004) Automated characterization of gene expression patterns with an atlas of the mouse brain. In: Proceedings of the 26th Annual International Conference of the IEEE EMBS;2004 September 1-5;San Francisco, California. Madison (Wisconsin): Omnipress. pp. 2917-2920.
21. Le WD, Xu P, Jankovic J, Jiang H, Appel SH, et al. (2003) Mutations in NR4A2 associated with familial Parkinson disease. Nat Genet 33: 85-89.
22. Polymeropoulos MH, Higgins JJ, Golbe LI, Johnson WG, Ide SE, et al. (1996) Mapping of a gene for Parkinson's disease to chromosome 4q21-q23. Science 274: 1197-1199.
23. Plante-Bordeneuve V, Taussig D, Thomas F, Said G, Wood NW, et al. (1997) Evaluation of four candidate genes encoding proteins of the dopamine pathway in familial and sporadic Parkinson's disease: Evidence for association of a DRD2 allele. Neurology 48: 1589-1593.
24. Haavik J, Toska K (1998) Tyrosine hydroxylase and Parkinson's disease. Mol Neurobiol 16: 285-309.
25. Smidt MP, Asbreuk CH, Cox JJ, Chen H, Johnson RL, et al. (2000) A second independent pathway for development of mesencephalic dopaminergic neurons requires Lmx1b. Nat Neurosci 3: 337-341.
26. Gaiter D, Buervenich S, Carmine A, Anvret M, Olson L (2003) ALDH1 mRNA: Presence in human dopamine neurons and decreases in substantia nigra in Parkinson's disease and in the ventral tegmental area in schizophrenia. Neurobiol Dis 14: 637-647.
27. Janz R, Sudhof TC (1999) SV2C is a synaptic vesicle protein with an unusually restricted localization: Anatomy of a synaptic vesicle protein family. Neuroscience 94: 1279-1290.
28. Stoldt V, Rademacher F, Kehren V, Ernst JF, Pearce DA, et al. (1996) Review: The Cet eukaryotic chaperonin subunits of Saccharomyces cerevisiae and other yeasts. Yeast 12: 523-529.
29. Yan HX, He YQ, Dong H, Zhang P, Zeng JZ, et al. (2002) Physical and functional interaction between receptor-like protein tyrosine phosphatase PCP-2 and beta-catenin. Biochemistry 41: 15854-15860.
30. Moeller C, Yaylaoglu MB, Alvarez-Bolado G, Thaller C, Eichele G (2002) Murine Lix1, a novel marker for substantia nigra, cortical layer 5, and hindbrain structures. Brain Res Gene Expr Patterns 1: 199-203.
31. Kakadiaris I, Bello M, Arunachalam S, Kang W, Ju T, et al. (2004) Landmark-driven, atlas-based segmentation of mouse brain tissue slices containing gene expression data. In: Barillot C, Haynor D, Hellier P, editors. Medical image computing and computer-assisted intervention - MICCAI 2004, 7th International Conference, Proceedings Part I; 26-29 September 2004, Rennes/Saint-Malo, France, pp. 192-199.
32. Visel A, Ahdidan J, Eichele G (2002) A gene expression map of the mouse brain: Genepaint.org - A database of gene expression patterns. In: Kotter R, editor. Neuroscience databases: A practical guide. Boston: Kluwer Academic Publishers, pp. 19-36
33. Herzig U, Cadenas C, Sieckmann F, Sierralta W, Thaller C, et al. (2001) Development of high-throughput tools to unravel the complexity of gene expression patterns in the mammalian brain. In: Bock G, Goode J, editors. Novartis Foundation Symposium: Complexity in biological information processing. Chicester: John Wiley and Sons. pp. 129-149
34. Yaylaoglu MB, Titmus A, Visel A, Alvarez-Bolado G, Thaller C, et al. (2005) Comprehensive expression atlas of fibroblast growth factors and their receptors generated by a novel robotic in situ hybridization platform. Dev Dyn. E-pub ahead of print.
35. Reymond A, Marigo V, Yaylaoglu MB, Leoni A, Ucla C, et al. (2002) Human chromosome 21 gene expression atlas in the mouse. Nature 420: 582-586.
36. Catmull E, Clark J (1978) Recursively generated B-spline surfaces on arbitrary topological meshes. Comput Aided Des 16: 350-355.
37. Warren J, Weimer H (2002) Subdivision methods for geometric design: A constructive approach. San Francisco: Morgan Kaufmann. 299 p.
38. Lu HC, She WC, Plas DT, Neumann PE, Janz R, et al. (2003) Adenylyl cyclase I regulates AMPA receptor trafficking during mouse cortical 'barrel' map development. Nat Neurosci 6: 939-947.
39. Van der Loos H, Welker E, Dorfl J, Rumo G (1986) Selective breeding for variations in patterns of mystacial vibrissae of mice. Bilaterally symmetrical strains derived from ICR stock. J Hered 77: 66-82.