Neuron-enriched gene expression patterns are regionally anti-correlated with oligodendrocyte-enriched patterns in the adult mouse and human brain

Frontiers in Neuroscience

Volumn , Issue 7 FEB, 2013, Pages

  Tan, Powell Patrick Cheng ^a   French, Leon ^a   Pavlidis, Paul ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Cell type; Evolution; Gene expression pattern; Glia; Neuron; Transcriptome

Indexed keywords

TRANSCRIPTOME;

ANIMAL TISSUE; ARTICLE; ASTROCYTE; BRAIN; CEREBELLUM; DIENCEPHALON; EPITHALAMUS; GENE EXPRESSION; HIPPOCAMPUS; HUMAN; HUMAN TISSUE; HYPOTHALAMUS; MALE; MEDULLA OBLONGATA; MESENCEPHALON; METENCEPHALON; MYELENCEPHALON; NERVE CELL; NONHUMAN; OLIGODENDROGLIA; PONS; PRINCIPAL COMPONENT ANALYSIS; TELENCEPHALON; THALAMUS;

EID: 84878883768     PISSN: 16624548     EISSN: 1662453X     Source Type: Journal    
DOI: 10.3389/fnins.2013.00005     Document Type: Article

References (33)

1. Azevedo, F. A. C., Carvalho, L. R. B., Grinberg, L. T., Farfel, J. M., Ferretti, R. E. L., Leite, R. E. P., et al. (2009). Equal numbers of neuronal and non-neuronal cells make the human brain an isometrically scaled-up primate brain. J. Comp. Neurol. 513, 532-541.
2. Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Methodol. 57, 289-300.
3. Blanger, M., Allaman, I., and Magistretti, P. J. (2011). Brain energy metabolism: focus on astrocyte-neuron metabolic cooperation. Cell Metab. 14, 724-738.
4. Cahoy, J. D., Emery, B., Kaushal, A., Foo, L. C., Zamanian, J. L., Christopherson, K. S., et al. (2008). A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J. Neurosci. 28, 264-278.
5. Cohen, S., and Greenberg, M. E. (2008). Communication between the synapse and the nucleus in neuronal development, plasticity, and disease. Annu. Rev. Cell Dev. Biol. 24, 183-209.
6. Dennis, G. Jr., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., et al. (2003). DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 4, P3.
7. Feher, J. (2012). Quantitative Human Physiology: An Introduction. Academic Press series in biomedical engineering. Elsevier Science and Technology, ISBN 9780123821638, 0123821649. URL http://textbooks.elsevier.com/web/productdetails.aspx?isbn=9780123821638
8. French, L., and Pavlidis, P. (2011). Relationships between gene expression and brain wiring in the adult rodent brain. PLoS Comput. Biol. 7:e1001049.
9. French, L., Tan, P. P. C., and Pavlidis, P. (2011). Large-scale analysis of gene expression and connectivity in the rodent brain: insights through data integration. Front. Neuroinform. 5:12.
10. Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., et al. (2012). An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489, 391-399.
11. Herculano-Houzel, S. (2009). The human brain in numbers: a linearly scaled-up primate brain. Front. Hum. Neurosci. 3:31.
12. Hunt, D., Mason, M. R. J., Campbell, G., Coffin, R., and Anderson, P. N. (2002). Nogo receptor mRNA expression in intact and regenerating CNS neurons. Mol. Cell. Neurosci. 20, 537-552.
13. Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., et al. (2011). Spatio-temporal transcriptome of the human brain. Nature 478, 483-489.
14. Lee, C.-K., Sunkin, S. M., Kuan, C., Thompson, C. L., Pathak, S., Ng, L., et al. (2008). Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data. Genome Biol. 9, R23.
15. Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168-176.
16. Liao, B.-Y., and Zhang, J. (2006). Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol. Biol. Evol. 23, 530-540.
17. Lockhart, D. J., and Barlow, C. (2001). Expressing what's on your mind: DNA arrays and the brain. Nat. Rev. Neurosci. 2, 63-68.
18. Miller, J. A., Horvath, S., and Geschwind, D. H. (2010). Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. Proc. Natl. Acad. Sci. U.S.A. 107, 12698-12703.
19. Nedergaard, M., Ransom, B., and Goldman, S. A. (2003). New roles for astrocytes: redefining the functional architecture of the brain. Trends Neurosci. 26, 523-530.
20. Ng, L., Bernard, A., Lau, C., Overly, C. C., Dong, H.-W., Kuan, C., et al. (2009). An anatomic gene expression atlas of the adult mouse brain. Nat. Neurosci. 12, 356-362.
21. Ng, L., Pathak, S., Kuan, C., Lau, C., Dong, H.-W., Sodt, A., et al. (2007). Neuroinformatics for genome-wide 3-d gene expression mapping in the mouse brain. IEEE/ACM Trans. Comput. Biol. Bioinform. 4, 382-393.
22. Oberheim, N. A., Takano, T., Han, X., He, W., Lin, J. H. C., Wang, F., et al. (2009). Uniquely hominid features of adult human astrocytes. J. Neurosci. 29, 3276-3287.
23. Oldham, M. C., Konopka, G., Iwamoto, K., Langfelder, P., Kato, T., Horvath, S., et al. (2008). Functional organization of the transcriptome in human brain. Nat. Neurosci. 11, 1271-1282.
24. Pavlidis, P., and Noble, W. S. (2001). Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol. 2, RESEARCH0042.
25. Pearson, K. (1901). On lines and planes of closest fit to systems of points in space. Philos. Mag. 2, 559-572.
26. R Core Team. (2012). R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing.
27. Sandberg, R., Yasuda, R., Pankratz, D. G., Carter, T. A., Del Rio, J. A., Wodicka, L., et al. (2000). Regional and strain-specific gene expression mapping in the adult mouse brain. Proc. Natl. Acad. Sci. U.S.A. 97, 11038-11043.
28. Sibille, E., Arango, V., Joeyen-Waldorf, J., Wang, Y., Leman, S., Surget, A., et al. (2008). Large-scale estimates of cellular origins of mRNAs: enhancing the yield of transcriptome analyses. J. Neurosci. Methods 167, 198-206.
29. Strand, A. D., Aragaki, A. K., Baquet, Z. C., Hodges, A., Cunningham, P., Holmans, P., et al. (2007). Conservation of regional gene expression in mouse and human brain. PLoS Genet. 3:e59.
30. Ward, J. H. (1963). Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc. 58, 236.
31. Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., et al. (2007). Database resources of the national center for biotechnology information. Nucleic Acids Res. 35, D5-D12.
32. Zapala, M. A., Hovatta, I., Ellison, J. A., Wodicka, L., Rio, J. A. D., Tennant, R., et al. (2005). Adult mouse brain gene expression patterns bear an embryologic imprint. Proc. Natl. Acad. Sci. U.S.A. 102, 10357-10362.
33. Zeng, H., Shen, E. H., Hohmann, J. G., Oh, S. W., Bernard, A., Royall, J. J., et al. (2012). Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures. Cell 149, 483-496.