Identification of a set of genes showing regionally enriched expression in the mouse brain
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- 作者：Cletus A D'Souza (1)
Vikramjit Chopra (1)
Richard Varhol (1)
Yuan-Yun Xie (2)
Slavita Bohacec (2)
Yongjun Zhao (1)
Lisa LC Lee (2)
Mikhail Bilenky (1)
Elodie Portales-Casamar (2)
An He (1)
Wyeth W Wasserman (2)
Daniel Goldowitz (2)
Marco A Marra (1)
Robert A Holt (2)
Elizabeth M Simpson (2)
Steven JM Jones (1) - 刊名：BMC Neuroscience
- 出版年：2008
- 出版时间：December 2008
- 年：2008
- 卷：9
- 期：1
- 全文大小：1623KB
- 参考文献：1. Strand AD, Aragaki AK, Baquet ZC, Hodges A, Cunningham P, Holmans P, Jones KR, Jones L, Kooperberg C, Olson JM: Conservation of regional gene expression in mouse and human brain. / PLoS genetics 2007,3(4):e59. CrossRef
2. Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE: Human-mouse genome comparisons to locate regulatory sites. / Nature genetics 2000,26(2):225鈥?28. CrossRef
3. Gotz J, Probst A, Spillantini MG, Schafer T, Jakes R, Burki K, Goedert M: Somatodendritic localization and hyperphosphorylation of tau protein in transgenic mice expressing the longest human brain tau isoform. / Embo J 1995,14(7):1304鈥?313.
4. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. / Science 1995,270(5235):484鈥?87. CrossRef
5. Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, / et al.: Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines. / Genome research 2007,17(1):108鈥?16. CrossRef
6. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE: Using the transcriptome to annotate the genome. / Nat Biotechnol 2002,20(5):508鈥?12. CrossRef
7. The Mouse Atlas of Gene Expression Project[mouseatlas.org" class="a-plus-plus">http://www.mouseatlas.org]
8. Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec 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. / Proceedings of the National Academy of Sciences of the United States of America 2005,102(51):18485鈥?8490. CrossRef
9. The Pleiades Promoter Project[http://www.pleiades.org/]
10. The NCBI PubMed Database[med.com" class="a-plus-plus">http://www.pubmed.com]
11. De Bruijn B, Martin J: Getting to the (c)ore of knowledge: mining biomedical literature. / Int J Med Inform 2002,67(1鈥?):7鈥?8. CrossRef
12. Scherf M, Epple A, Werner T: The next generation of literature analysis: integration of genomic analysis into text mining. / Brief Bioinform 2005,6(3):287鈥?97. CrossRef
13. The Allen Brain Atlas Database[http://www.allenbrainatlas.org/]
14. Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, / et al.: Genome-wide atlas of gene expression in the adult mouse brain. / Nature 2007,445(7124):168鈥?76. CrossRef
15. McCarthy M: Allen Brain Atlas maps 21,000 genes of the mouse brain. / Lancet Neurol 2006,5(11):907鈥?08. CrossRef
16. Simone NL, Bonner RF, Gillespie JW, Emmert-Buck MR, Liotta LA: Laser-capture microdissection: opening the microscopic frontier to molecular analysis. / Trends Genet 1998,14(7):272鈥?76. CrossRef
17. Nakai J, Fujita S: Early events in the histo- and cytogenesis of the vertebrate CNS. / The International journal of developmental biology 1994,38(2):175鈥?83.
18. The GENSAT Database[http://www.gensat.org]
19. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, / et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. / Nature genetics 2000,25(1):25鈥?9. CrossRef
20. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, / et al.: Initial sequencing and comparative analysis of the mouse genome. / Nature 2002,420(6915):520鈥?62. CrossRef
21. Liao BY, Zhang J: Evolutionary conservation of expression profiles between human and mouse orthologous genes. / Molecular biology and evolution 2006,23(3):530鈥?40. molbev/msj054">CrossRef
22. Machon O, Bout CJ, Backman M, Rosok O, Caubit X, Fromm SH, Geronimo B, Krauss S: Forebrain-specific promoter/enhancer D6 derived from the mouse Dach1 gene controls expression in neural stem cells. / Neuroscience 2002,112(4):951鈥?66. CrossRef
23. Brochier C, Gaillard MC, Diguet E, Caudy N, Dossat C, Segurens B, Wincker P, Roze E, Caboche J, Hantraye P, / et al.: Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models. / Physiological genomics 2008,33(2):170鈥?79. mics.00125.2007">CrossRef
24. Zapala MA, Hovatta I, Ellison JA, Wodicka L, Del Rio JA, Tennant R, Tynan W, Broide RS, Helton R, Stoveken BS, / et al.: Adult mouse brain gene expression patterns bear an embryologic imprint. / Proceedings of the National Academy of Sciences of the United States of America 2005,102(29):10357鈥?0362. CrossRef
25. Sugino K, Hempel CM, Miller MN, Hattox AM, Shapiro P, Wu C, Huang ZJ, Nelson SB: Molecular taxonomy of major neuronal classes in the adult mouse forebrain. / Nat Neurosci 2006,9(1):99鈥?07. CrossRef
26. Letwin NE, Kafkafi N, Benjamini Y, Mayo C, Frank BC, Luu T, Lee NH, Elmer GI: Combined application of behavior genetics and microarray analysis to identify regional expression themes and gene-behavior associations. / J Neurosci 2006,26(20):5277鈥?287. CrossRef
27. Stansberg C, Vik-Mo AO, Holdhus R, Breilid H, Srebro B, Petersen K, Jorgensen HA, Jonassen I, Steen VM: Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation. / BMC genomics 2007, 8:94. CrossRef
28. Fang H, Tong W, Shi L, Jakab RL, Bowyer JF: Classification of cDNA array genes that have a highly significant discriminative power due to their unique distribution in four brain regions. / DNA and cell biology 2004,23(10):661鈥?74. CrossRef
29. Suzuki H, Okunishi R, Hashizume W, Katayama S, Ninomiya N, Osato N, Sato K, Nakamura M, Iida J, Kanamori M, / et al.: Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR. / FEBS letters 2004,573(1鈥?):214鈥?18. CrossRef
30. Gray PA, Fu H, Luo P, Zhao Q, Yu J, Ferrari A, Tenzen T, Yuk DI, Tsung EF, Cai Z, / et al.: Mouse brain organization revealed through direct genome-scale TF expression analysis. / Science 2004,306(5705):2255鈥?257. CrossRef
31. Sandelin A, Wasserman WW: Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. / Journal of molecular biology 2004,338(2):207鈥?15. mb.2004.02.048">CrossRef
32. Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ: ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. / Bioinformatics (Oxford, England) 2006,22(5):637鈥?40. matics/btk027">CrossRef
33. Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, Ticoll A, Snoddy J, Wasserman WW: PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. / Genome Biol 2007,8(10):R207. CrossRef
34. Li J, Liu ZJ, Pan YC, Liu Q, Fu X, Cooper NG, Li YX, Qiu MS, Shi TL: Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain. / Genome Biol 2007,8(11):R244. CrossRef
35. Polli JW, Kincaid RL: Expression of a calmodulin-dependent phosphodiesterase isoform (PDE1B1) correlates with brain regions having extensive dopaminergic innervation. / J Neurosci 1994,14(3 Pt 1):1251鈥?261.
36. Sakurai T, Moriguchi T, Furuya K, Kajiwara N, Nakamura T, Yanagisawa M, Goto K: Structure and function of human prepro-orexin gene. / The Journal of biological chemistry 1999,274(25):17771鈥?7776. CrossRef
37. Waleh NS, Apte-Deshpande A, Terao A, Ding J, Kilduff TS: Modulation of the promoter region of prepro-hypocretin by alpha-interferon. / Gene 2001,262(1鈥?):123鈥?28. CrossRef
38. Peters DG, Kassam AB, Yonas H, O'Hare EH, Ferrell RE, Brufsky AM: Comprehensive transcript analysis in small quantities of mRNA by SAGE-lite. / Nucleic acids research 1999,27(24):e39. CrossRef
39. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. / Genome research 1998,8(3):186鈥?94.
40. Robertson N, Oveisi-Fordorei M, Zuyderduyn SD, Varhol RJ, Fjell C, Marra M, Jones S, Siddiqui A: DiscoverySpace: an interactive data analysis application. / Genome Biol 2007,8(1):R6. CrossRef
41. The NCBI Reference Sequence Collection[m.nih.gov/RefSeq" class="a-plus-plus">http://www.ncbi.nlm.nih.gov/RefSeq]
42. The Mammalian Gene Collection[mgc.nci.nih.gov" class="a-plus-plus">http://mgc.nci.nih.gov]
43. The Ensembl Database[mbl.org" class="a-plus-plus">http://www.ensembl.org]
44. Audic S, Claverie JM: The significance of digital gene expression profiles. / Genome research 1997,7(10):986鈥?95.
45. Greenberg DS: National Institutes of Health moves ahead with "PubMed Central". / Lancet 1999,354(9183):1009. CrossRef
46. Berman JJ: Improved Medical Sentence Parser. / Arch Pathol Lab Med 2003, 127:789鈥?13.
47. Maere S, Heymans K, Kuiper M: BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. / Bioinformatics (Oxford, England) 2005,21(16):3448鈥?449. matics/bti551">CrossRef
48. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. / Genome research 2003,13(11):2498鈥?504. CrossRef
49. Benjamini Y, Hochberg Y: Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. / Journal of the Royal Statistical Society, Series B 1995, 57:289鈥?00. - 作者单位：Cletus A D'Souza (1)
Vikramjit Chopra (1)
Richard Varhol (1)
Yuan-Yun Xie (2)
Slavita Bohacec (2)
Yongjun Zhao (1)
Lisa LC Lee (2)
Mikhail Bilenky (1)
Elodie Portales-Casamar (2)
An He (1)
Wyeth W Wasserman (2)
Daniel Goldowitz (2)
Marco A Marra (1)
Robert A Holt (2)
Elizabeth M Simpson (2)
Steven JM Jones (1)
1. Genome Sciences Centre, British Columbia Cancer Agency, 570 West 7th Ave 鈥?Suite 100, V5Z 4E6, Vancouver, BC, Canada
2. Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Ave., V5Z 4H4, Vancouver, BC, Canada
文摘
Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters (< 4 kb) that drive gene expression in specific brain regions or cell-types of therapeutic interest. Our goal was to first identify genes displaying regionally enriched expression in the mouse brain so that promoters designed from orthologous human genes can then be tested to drive reporter expression in a similar pattern in the mouse brain. Results We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas in situ hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology. Conclusion Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression.