Using evolutionary conserved modules in gene networks as a strategy to leverage high throughput gene expression queries

PLoS ONE

Volumn 5, Issue 9, 2010, Pages 1-14

  Serb, Jeanne M ^a   Orr, Megan C ^b   Heather West Greenlee, M ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b Iowa State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BONE MORPHOGENETIC PROTEIN 4; CALPAIN 2; DYNEIN ADENOSINE TRIPHOSPHATASE; FATTY ACID BINDING PROTEIN; FATTY ACID BINDING PROTEIN 5; GLI KRUPPEL FAMILY MEMBER; GLUTATHIONE TRANSFERASE; GUANINE NUCLEOTIDE BINDING PROTEIN; HEAT SHOCK TRANSCRIPTION FACTOR 1; MEIS HOMEOBOX 2; NOTCH1 RECEPTOR; PROTEIN ATOH7; PROTEIN DACH1; PROTEIN EYA1; PROTEIN EYA2; PROTEIN EYA3; PROTEIN TYROSINE KINASE; SONIC HEDGEHOG PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR HES 1; TRANSCRIPTION FACTOR OTX; TRANSCRIPTION FACTOR OTX1; TRANSCRIPTION FACTOR PAX6; TRANSCRIPTION FACTOR SIX1; TRANSCRIPTION FACTOR SIX2; TRANSCRIPTION FACTOR SIX3; TRANSCRIPTION FACTOR SIX6; UNCLASSIFIED DRUG; WNT INHIBITORY FACTOR 1; WNT4 PROTEIN; PROTEIN;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BRAIN DEVELOPMENT; CELL DIFFERENTIATION; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE EXPRESSION; GENE REGULATORY NETWORK; GENETIC CONSERVATION; HIGH THROUGHPUT SCREENING; MOUSE; NONHUMAN; PROTEIN EXPRESSION; PROTEIN FUNCTION; RETINA CELL; RETINA DEVELOPMENT; ALGORITHM; ANIMAL; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR EVOLUTION; RETINA;

DROSOPHILA MELANOGASTER;

ALGORITHMS; ANIMALS; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE REGULATORY NETWORKS; MICE; PROTEINS; RETINA;

EID: 77958549598     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012525     Document Type: Article

References (108)

1. Hartemink AJ, Gifford DK, Jaakkola TS, Young RA (2002) Combining location and expression data for principled discovery of genetic regulatory network models. Pacific Symposium on Biocomputing 2002: 437-449.
2. Markowetz F, Spang R (2007) Inferring cellular networks-a review. BMC Bioinformatics 8 Suppl 6: S5.
3. Magwene PM, Kim J (2004) Estimating genomic coexpression networks using first-order conditional independence. Genome Biology 5: R100.
4. Butte A, Kohane I (2003) Relevance networks: a first step towards finding genetic regulatory networks within microarray data. In: Parmigiani G, Garret ES, Irizarry RA, Zeger SL, eds. The analysis of gene expression data. New York: Springer.
5. Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian networks to analyze expression data. Journal of Computing Biology 7: 601-620.
6. Johnson RA, Wichern DW (2002) Applied multivariate statistical analysis Prentice Hall.
7. Hecker LA, Alcon TA, Honavar VG, West Greenlee MH (2008) Using a seed-network to query multiple large-scale gene expression datasets from the developing retina in order to identify and prioritize experimental targets. Bioinformatics and Biology Insights 2008: 91-102.
8. Pappu KS, Mardon G (2004) Genetic control of retinal specification and determination in Drosophila. International Journal of Developmental Biology 48: 913-924 SI.
9. Land MF, Nilsson D-E (2006) Animal Eyes Oxford University Press.
10. Livesey FJ, Cepko CL (2001) Vertebrate neural cell-fate determination: lessons from the retina. Nature Reviews 2: 109-118.
11. Walls GL (1967) The vertebrate eye and its adaptive radiation. New York: Haffner Publishing Company. 785 p.
12. Quiring R, Walldorf U, Kloter U, Gehring WJ (1994) Homology of the eyeless gene of Drosophila to the small eye gene in mice and aniridia in humans. Science 265: 785-789.
13. Xu P, Woo I, Her HB, D.R. Maas R L (1997) Mouse Eya homologues of the Drosophila eyes absent gene require Pax6 for expression in lens and nasal placodes. Development 124: 219-231.
14. Brown NL, Kanekar S, Vetter ML, Tucker PK, Gemza DL, et al. (1998) Math5 encodes a murine basic helix-loop-helix transcription factor expressed during early stages of retinal neurogenesis. Development 125: 4821-4833.
15. Niiya A, Ohto H, Kawakami K, Araki M (1998) Localization of Six4/AREC3 in the developing mouse retina; implications in mammalian retinal development. Experimental Eye Research 67: 699-707.
16. Chen R, Halder G, Zhang Z, Mardon G (1999) Signaling by the TGF-beta homolog decapentaplegic functions reiteratvely within the network of genes controlling retinal cell fate determination in Drosophila. Development 126: 935-943.
17. Wawersik S, Maas RL (2000) Vertebrate eye development as modeled in Drosophila. Human Molecular Genetics 9: 917-925.
18. Gehring WJ, Ikeo K (1999) Pax6: mastering eye morphogenesis and eye evolution. TIG 15: 371-377.
19. Donner AL, Maas RL (2004) Conservation and non-conservation of genetic pathways in eye specificiation. Int J Dev Biol 48: 743-753.
20. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, et al. (2004) Genomic analysis of mouse retinal development. PLoS Biology 2.
21. Zhang SS, Xu X, Liu MG, Zhao H, Soares MB, et al. (2006) A biphasic pattern of gene expression during mouse retina development. BMC Developmental Biology 6: 48.
22. Liu J, Wang J, Huang Q, Higdon J, Magdaleno S, et al. (2006) Gene expression profiles of mouse retinas during the second and third postnatal weeks. Brain Research 1098: 113-125.
23. Dorrell MI, Aguilar E, Weber C, Friedlander M (2004) Global gene expression analysis of the developing postnatal mouse retina. Investigative Ophthalmology and Visual Science 45: 1009-1019.
24. Ahmad H, Singh SV, Medh RD, Ansari GA, Kurosky A, et al. (1988) Differential expression of alpha, mu and pi classes of isozymes of glutathione S-transferase in bovine lens, cornea, and retina. Archives of Biochemistry and Biophysics 266: 416-426.
25. Ahuja P, Caffé AR, Ahuja S, Ekström P, van Veen T (2005) Decreased glutathione transferase levels in rd1/rd1 mouse retina: replenishment protects photoreceptors in retinal explants. Neuroscience 131: 935-943.
26. Allen GW, Liu J, Kirby MA, De León M (2001) Induction and axonal localization of epitheliałepidermal fatty acid-binding protein in retinal ganglion cells are associated with axon development and regeneration. Journal of Neuroscience Research 66: 396-405.
27. Amrein L, Barraud P, Daniel JY, Perel Y, Landry M (2005) Expression patterns of nm23 genes during mouse organogenesis. Cell Tissue Research 322: 365-378.
28. Asano T, Shinohara H, Morishita R, Ueda H, Kawamura N, et al. (2001) Selective localization of G protein gamma5 subunit in the subventricular zone of the lateral ventricle and rostral migratory stream of the adult rat brain. Journal of Neurochemistry 79: 1129-1135.
29. Azuma M, Shearer TR (2008) The role of calcium-activated protease calpain in experimental retinal pathology. Survey of Opthalmology 53: 150-163.
30. Birgbauer E, Cowan CA, Sretavan DW, Henkemmeyer M (2000) Kinase independent function of EphB receptors in retinal axon pathfinding to the optic disc from dorsal but not ventral retina. Development 127: 1231-1241.
31. Border BG, Lin SC, Griffin WS, Pardue S, Morrison-Bogorad M (1993) Alterations in actin-binding beta-thymosin expression accompany neuronal differentiation and migration in rat cerebellum. Journal of Neurochemistry 61: 2104-2014.
32. Bult C, Eppig JT, Richardson JE, Blake JA, Group atmot MGD (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Research 36: D724-728.
33. Carpintero P, Anadon R, Gomez-Marquez J (1999) Expression of the thymosin beta10 gene in normal and kainic acid-treated rat forebrain. Brain Research Mol Brain Res 18: 141-146.
34. Charrier E, Mosinger B, Meissirel C, Aguera M, Rogemond V, et al. (2006) Transient alterations in granule cell proliferation, apoptosis and migration in postnatal developing cerebellum of CRMP1-/- mice. Genes to Cells 11: 1337-1352.
35. Chen Y, Tang BL (2006) The amyloid precursor protein and postnatal neurogenesis/neuroregeneration. Biochemical and Biophysical Research Communications 341: 1-5.
36. Corbetta S, Gualdoni S, Ciceri G, Monari M, Zuccaro E, et al. (2009) Essential role of Rac1 and Rac3 GTPases in neuronal development. FASEB J 23: 1347-1357.
37. Davis JA, Reed RR (1996) Role of Olf-1 and Pax-6 transcription factors in neurodevelopment. Journal of Neuroscience 16: 5082-5094.
38. de Brouwer AP, Williams KL, Duley JA, van Kuilenburg AB, Nabuurs SB, et al. (2007) Arts syndrome is caused by loss-of-function mutations in PRPS1. American Journal of Human Genetics 81: 507-518.
39. Dyer MA, Cepko CL (2001) p27Kip1 and p57Kip2 regulate proliferation in distinct retinal progenitor cell populations. Journal of Neuroscience 21: 4259-4271.
40. Dyer MA, Cepko CL (2001) The p57Kip2 cyclin kinase inhibitor is expressed by a restricted set of amacrine cells in the rodent retina. Journal of Comparative Neurology 429: 601-614.
41. El-Khodor BF, Kholodilov NG, Yarygina O, Burke RE (2001) The expression of mRNAs for the proteasome complex is developmentally regulated in the rat mesencephalon. Brain Research, Developmental Brain Research 129: 47-56.
42. Ewing JF, Maines MD (1995) Immunohistochemical localization of biliverdin reductase in rat brain: age related expression of protein and transcript. Brain Research 672: 29-41.
43. Fullerton MD, Hakimuddin F, Bakovic M (2007) Developmental and metabolic effects of disruption of the mouse CTP:phosphoethanolamine cytidylyltransferase gene (Pcyt2). Molecular Cellular Biology 27: 3327-3336.
44. Gu C, Zhou W, Puthenveedu MA, Xu M, Jan YN, et al. (2006) The microtubule plus-end tracking protein EB1 is required for Kv1 voltage-gated K+ channel axonal targeting. Neuron 52: 803-816.
45. Guénette S, Chang Y, Hiesberger T, Richardson JA, Eckman CB, et al. (2006) Essential roles for the FE65 amyloid precursor protein-interacting proteins in brain development. EMBO Journal 25: 420-431.
46. Hou ST, Jiang SX, Desbois A, Huang D, Kelly J, et al. (2006) Calpain-cleaved collapsin response mediator protein-3 induces neuronal death after glutamate toxicity and cerebral ischemia. Journal of Neuroscience 26: 2241-2209.
47. Hwang IK, Yoo KY, Kim DW, Kim SY, Park JH, et al. (2008) Ischemia-induced ribosomal protein S3 expressional changes and the neuroprotective effect against experimental cerebral ischemic damage. Journal of Neuroscience Research 86: 1823-1835.
48. Ivanov D, Dvoriantchikova G, Barakat DJ, Nathanson L, Shestopalov VI (2008) Differential gene expression profiling of large and small retinal ganglion cells. Journal of Neuroscience Methods 174: 10-17.
49. Jones SE, Jomary C, Grist J, Stewart HJ, Neal MJ (2000) Identification by array screening of altered nm23-M2/PuF mRNA expression in mouse retinal degeneration. Molecular Cell Biol Res Commun 4: 20-25.
50. Kanan Y, Moiseyev G, Agarwal N, Ma JX, Al-Ubaidi MR (2007) Light induces programmed cell death by activating multiple independent proteases in a cone photoreceptor cell line. Investigative Ophthalmology and Visual Science 48: 40-51.
51. Kasai T, Inoue M, Koshiba S, Yabuki T, Aoki M, et al. (2004) Solution structure of a BolA-like protein from Mus musculus. Protein Science 13: 545-548.
52. Kim HJ, Sohn KM, Shy ME, Krajewski KM, Hwang M, et al. (2007) Mutations in PRPS1, which encodes the phosphoribosyl pyrophosphate synthetase enzyme critical for nucleotide biosynthesis, cause hereditary peripheral neuropathy with hearing loss and optic neuropathy (cmtx5). American Journal of Human Genetics 81: 552-558.
53. Koyabu Y, Nakata K, Mizugishi K, Aruga J, Mikoshiba K (2001) Physical and functional interactions between Zic and Gli proteins. Journal of Biological Chemistry 276: 6889-6892.
54. Lai M, Wang F, Rohan JG, Maeno-Hikichi Y, Chen Y, et al. (2005) A tctex1-Ca2+ channel complex for selective surface expression of Ca2+ channels in neurons. Nature Neuroscience 8: 435-442.
55. Lee R, Petros TJ, Mason CA (2008) Zic2 regulates retinal ganglion cell axon avoidance of ephrinB2 through inducing expression of the guidance receptor EphB1. Journal of Neuroscience 28: 5910-5919.
56. Lee SS, Seo HS, Choi SJ, Park HS, Lee JY, et al. (2003) Characterization of the two genes differentially expressed during development in human fetal astrocytes. Yonsei Medical Journal 44: 1059-1068.
57. Lim YS, McLaughlin T, Sung TC, Santiago A, Lee KF, et al. (2008) p75(NTR) mediates ephrin-A reverse signaling required for axon repulsion and mapping. Neuron 59: 746-758.
58. Liu JW, Almaguel FG, Bu L, De Leon DD, De Leon M (2008) Expression of E-FABP in PC12 cells increases neurite extension during differentiation: involvement of n-3 and n-6 fatty acids. Journal of Neurochemistry 106: 2015-2029.
59. Lobo MK, Yeh C, Yang XW (2008) Pivotal role of early B-cell factor 1 in development of striatonigral medium spiny neurons in the matrix compartment. Journal of Neuroscience Research 86: 2134-2146.
60. McKee AE, Minet E, Stern C, Riahi S, Stiles CD, et al. (2005) A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. BMC Developmental Biology 5: 14.
61. Miller NL, Wevrick R, Mellon PL (2009) Necdin, a Prader-Willi syndrome candidate gene, regulates gonadotropin-releasing hormone neurons during development. Human Molecular Genetics 18: 248-260.
62. Mitchell DC, Bryan BA, Liu JP, Liu WB, Zhang L, et al. (2007) Developmental expression of three small GTPases in the mouse eye. Molecular Vision 13: 1144-1153.
63. Monaghan MM, Trimmer JS, Rhodes KJ (2001) Experimental localization of Kv1 family voltage-gated K+ channel alpha and beta subunits in rat hippocampal formation. Journal of Neuroscience 21: 5973-5783.
64. Munemasa Y, Kim SH, Ahn JH, Kwong JM, Caprioli J, et al. (2008) Protective effect of thioredoxins 1 and 2 in retinal ganglion cells after optic nerve transection and oxidative stress. Investigative Ophthalmology and Visual Science 49: 3535-3543.
65. Nagahama H, Hatakeyama S, Nakayama K, Nagata M, Tomita K, et al. (2001) Spatial and temporal expression patterns of the cyclin-dependent kinase (CDK) inhibitors p27Kip1 and p57Kip2 during mouse development. Anatomy and Embryology 203: 77-87.
66. Nakajima E, David LL, Bystrom C, Shearer TR, Azuma M (2006) Calpain-specific proteolysis in primate retina: Contribution of calpains in cell death. Investigative Ophthalmology and Visual Science 47: 5469-5475.
67. Nakazawa T, Nakano I, Furuyama T, Morii H, Tamai M, et al. (2000) The SCG10-related gene family in the developing rat retina: persistent expression of SCLIP and stathmin in mature ganglion cell layer. Brain Research 861: 399-407.
68. Okazaki Y, Furuno M, Kasukawa T, Acachi J, Team. FCRGERGPII (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
69. Panahian N, Huang T, Maines MD (1999) Enhanced neuronal expression of the oxidoreductase-biliverdin reductase-after permanent focal cerebral ischemia. Brain Research 850: 1-13.
70. Quach TT, Massicotte G, Belin MF, Honnorat J, Glasper ER, et al. (2008) CRMP3 is required for hippocampal CA1 dendritic organization and plasticity. FASEB J 22: 401-409.
71. Quach TT, Mosinger BJ, Ricard D, Copeland NG, Gilbert DJ, et al. (2000) Collapsin response mediator protein-3/unc-33-like protein-4 gene: organization, chromosomal mapping and expression in the developing mouse brain. Gene 242: 175-182.
72. Rosenmund C, Sigler A, Augustin I, Reim K, Brose N, et al. (2002) Differential control of vesicle priming and short-term plasticity by Munc13 isoforms. Neuron 33: 411-424.
73. Sánchez-Camacho C, Bovolenta P (2008) Autonomous and non-autonomous Shh signalling mediate the in vivo growth and guidance of mouse retinal ganglion cell axons. Development 135: 3531-3541.
74. Sharma AK, Rohrer B (2007) Sustained elevation of intracellular CGMP causes oxidative stress triggering calpain-mediated apoptosis in photoreceptor degeneration. Current Eye Research 32: 259-269.
75. Shaw RM, Fay AJ, Puthenveedu MA, von Zastrow M, Jan YN, et al. (2007) Microtubule plus-end-tracking proteins target gap junctions directly from the cell interior to adherens junctions. Cell 128: 547-560.
76. Shichiri M, Ishimaru S, Ota T, Nishikawa T, Isogai T, et al. (2003) Salusins: newly identified bioactive peptides with hemodynamic and mitogenic activities. Nature Medicine 9: 1166-1172.
77. Shkumatava A, Neumann CJ (2005) Shh directs cell-cycle exit by activating p57Kip2 in the zebrafish retina. EMBO Reports 6: 563-569.
78. Suh LH, Oster SF, Soehrman SS, Grenningloh G, Sretavan DW (2004) L1/ Laminin modulation of growth cone response to EphB triggers growth pauses and regulates the microtubule destabilizing protein SCG10. Journal of Neuroscience 24: 1976-1986.
79. Sweeney KJ, Clark GD, Prokscha A, Dobyns WB, Eichele G (2000) Lissencephaly associated mutations suggest a requirement for the PAFAH1B heterotrimeric complex in brain development. Mechanisms of Development 92: 263-271.
80. Tang YP, Wade J (2006) Sexually dimorphic expression of the genes encoding ribosomal proteins L17 and L37 in the song control nuclei of juvenile zebra finches. Brain Research 1126: 102-108.
81. Thies E, Davenport RW (2003) Independent roles of Rho-GTPases in growth cone and axonal behavior. Journal of Neurobiology 54: 358-369.
82. Trimarchi JM, Stadler MB, Roska B, Billings N, Sun B, et al. (2007) Molecular heterogeneity of developing retinal ganglion and amacrine cells revealed through single cell gene expression profiling. Journal of Comparative Neurology 502: 1047-1065.
83. Tsim TY, Wong EY, Leung MS, Wong CC (2004) Expression of axon guidance molecules and their related genes during development and sexual differentiation of the olfactory bulb in rats. Neuroscience 123: 951-965.
84. Varoqueaux F, Sigler A, Rhee JS, Brose N, Enk C, et al. (2002) Total arrest of spontaneous and evoked synaptic transmission but normal synaptogenesis in the absence of Munc13-mediated vesicle priming. Proceedings of the National Academy of Science USA 99: 9037-9042.
85. Wilson MJ, Salata MW, Susalka SJ, Pfister KK (2001) Light chains of mammalian cytoplasmic dynein: identification and characterization of a family of LC8 light chains. Cell Motil Cytoskeleton 49: 229-240.
86. Young-Pearse TL, Bai J, Chang R, Zheng JB, LoTurco JJ, et al. (2007) A critical function for beta-amyloid precursor protein in neuronal migration revealed by in utero RNA interference. Journal of Neuroscience 27: 14459-14469.
87. Ready DF, Hanson TE, Benzer S (1976) Development of the Drosophila retina, a neurocrystalline lattice. Developmental Biology 53: 217-240.
88. Liu YH, Jakobsen JS, Valentin G, Amarantos I, Gilmour DT, et al. (2009) A systematic analysis of Tinman function reveals Eya and JAK-STAT signaling as essential regulators of muscle development. Developmental Cell 16: 280-291.
89. Hamada H, Meno C, Watanabe D, Saijoh Y (2002) Establishment of vertebrate left-right asymmetry. Nature Reviews Genetics 3: 103-113.
90. Bell R, Hubbard A, Chettier R, Chen D, Miller JP, et al. (2009) A human protein interaction network shows conservation of aging processes between human and invertebrate species. PLos Genetics 5: e1000414.
91. Sinclair A, Smith C, Western P, McClive P (2002) A comparative analysis of vertebrate sex determination. In: Chadwick D, Goode J, eds. The Genetics and Biology of Sex Determination, Novartis Foundation Symposium. Chichester: John Wiley& Sons. pp 102-114.
92. Kielbasa SM, Vingron M (2008) Transcriptional autoregulatory loops are highly conserved in vertebrate evolution. PLoS ONE 3: e3210
93. FlyBase http://flybase.org/.
94. Informatics MG http://www.informatics.jax.org.
95. Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, et al. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Research 34(Database issue): D572-580.
96. Ruan J, Li H, Chen Z, Coghlan A, Coin LJM, et al. (2008) TreeFam: 2008 Update. Nucleic Acids Research 36(Database issue): D735-740.
97. HomoloGene http://www.ncbi.nlm.nih.gov/homologene.
98. Manfroid I, Caubit X, Kerridge S, Fasano L (2004) Three putative murine Teashirt orthologues specify trunk structures in Drosophila in the same way as the Drosophila teashirt gene. Development 131: 1065-1073.
99. van Heyningen V, Williamson K (2002) PAX6 in sensory development. Human Molecular Genetics 11: 1161-1167.
100. Brown NL, Patel S, Brzezinski J, Glaser T (2001) Math5 is required for retinal ganglion cell and optic nerve formation. Development 128: 2497-2508.
101. Wang SW, Kim BS, Ding K, Wang H, Sun D, et al. (2001) Requirement for Math5 in the development of retinal ganglion cells. Genes& Development 15: 24-29.
102. Seimiya M, Gehring WJ (2000) The Drosophila homeobox gene optix is capable of inducing ectopic eyes by an eyeless-independent mechanism. Development 127: 1879-1886.
103. Yona G, Dirks W, Rahman S, Lin DM (2006) Effective similarity measures for expression profiles. Bioinformatics 22: 1616-1622.
104. Griffith OL, Pleasance ED, Fulton DL, Oveisi M, Ester M, et al. (2005) Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression. Genomics 86: 476-488.
105. Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, et al. (2005) Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436: 861-865.
106. Lee HK, Sajdak J, Qin J, Pavlidis P (2004) Coexpression analysis of human genes across many microarray data sets. Genome Research 14: 1085-1094.
107. PubMed http://www.ncbi.nlm.nih.gov/pubmed/.
108. Bult C, Eppig JT, Richardson JE, Blake JA, Group atmotMGD (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Research 36: D724-728.