Differentially expressed genes strongly correlated with femur strength in rats

Genomics

Volumn 94, Issue 4, 2009, Pages 257-262

  Alam, Imranul ^a   Sun, Qiwei ^a   Koller, Daniel L ^b   Liu, Lixiang ^b   Liu, Yunlong ^b   Edenberg, Howard J ^b   Li, Jiliang ^b   Foroud, Tatiana ^b   Turner, Charles H ^a  

^a Indiana University Purdue University Indianapolis   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

Femur strength; Gene expression; Microarray; Osteoporotic fracture; QTLs

Indexed keywords

ALPHA INTERFERON; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE; TUMOR NECROSIS FACTOR;

ANIMAL TISSUE; ARTICLE; BONE STRENGTH; CHROMOSOME 1Q; FEMALE; FEMUR; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; MICROARRAY ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RAT; RAT STRAIN;

ALGORITHMS; ALLELES; ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES, MAMMALIAN; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CROSSES, GENETIC; FEMALE; FEMUR; GENE EXPRESSION; GENE REGULATORY NETWORKS; GENETIC LINKAGE; GENETIC MARKERS; GENOME; GENOTYPE; HOMOZYGOTE; MICROARRAY ANALYSIS; MICROSATELLITE REPEATS; MULTIGENE FAMILY; PHENOTYPE; QUANTITATIVE TRAIT LOCI; RATS; RATS, INBRED F344; RATS, INBRED LEW; RATS, INBRED STRAINS; RNA; RNA, MESSENGER; STRESS, MECHANICAL;

ANIMALIA; RATTUS;

EID: 70249106321     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2009.05.008     Document Type: Article

References (44)

1. Kanis J.A., Melton L.J., Christiansen C., Johnston C.C., and Khaltaev N. The diagnosis of osteoporosis. J. Bone. Miner. Res. 9 (1994) 1137-1141
2. Cummings S.R., Black D.M., Nevitt M.C., Browner W., Cauley J., Ensrud K., Genant H.K., Palermo L., Scott J., and Vogt T.M. Bone density at various sites for prediction of hip fractures. The Study of Osteoporotic Fractures Research Group, Lancet 341 (1993) 72-75
3. Faulkner K.G., Cummings S.R., Black D., Palermo L., Gluer C.C., and Genant H.K. Simple measurement of femoral geometry predicts hip fracture: the study of osteoporotic fractures. J. Bone. Miner. Res. 8 (1993) 1211-1217
4. Peacock M., Turner C.H., Liu G., Manatunga A.K., Timmerman L., and Johnston C.C. Better discrimination of hip fracture using bone density, geometry and architecture. Osteoporos. Int. 5 (1995) 167-173
5. Arden N.K., Baker J., Hogg C., Bann K., and Spector T.D. The heritability of bone mineral density, ultrasound of the calcaneus and hip axis length: a study of postmenopausal twins. J. Bone Miner. Res. 11 (1996) 530-534
6. Garnero P., Arden N.K., Griffiths G., Delmas P.D., and Spector T.D. Genetic influence on bone turnover in postmenopausal twins. J. Clin. Endocrinol. Metab. 81 (1996) 140-146
7. Peacock M., Turner C.H., Econs M.J., and Foroud T. Genetics of osteoporosis. Endocr. Rev. 23 (2002) 378-383
8. Ralston S.H. Genetic determinants of osteoporosis. Curr. Opin. Rheumatol. 17 (2005) 475-479
9. Karasik D., Shimabuku N.A., Zhou Y., Zhang Y., Cupples L.A., Kiel D.P., and Demissie S. A genome wide linkage scan of metacarpal size and geometry in the Framingham Study. Am. J. Hum. Biol. 20 (2008) 663-670
10. Streeten E.A., Beck T.J., O'Connell J.R., Rampersand E., McBride D.J., Takala S.L., Pollin T.I., Uusi-Rasi K., Mitchell B.D., and Shuldiner A.R. Autosome-wide linkage analysis of hip structural phenotypes in the Old Order Amish. Bone 43 (2008) 607-612
11. Shen H., Long J.R., Xiong D.H., Guo Y.F., Xiao P., Liu Y.Z., Zhao L.J., Liu Y.J., Deng H.Y., Li J.L., Recker R.R., and Deng H.W. A genomewide scan for quantitative trait loci underlying areal bone size variation in 451 Caucasian families. J. Med. Genet. 43 (2006) 873-880
12. Deng H.W., Xu F.H., Huang Q.Y., Shen H., Deng H., Conway T., Liu Y.J., Liu Y.Z., Li J.L., Zhang H.T., Davies K.M., and Recker R.R. A whole-genome linkage scan suggests several genomic regions potentially containing quantitative trait loci for osteoporosis. J. Clin. Endocrinol. Metab. 87 (2002) 5151-5159
13. Deng H.W., Xu F.H., Liu Y.Z., Shen H., Deng H., Huang Q.Y., Liu Y.J., Conway T., Li J.L., Davies K.M., and Recker R.R. A whole-genome linkage scan suggests several genomic regions potentially containing QTLs underlying the variation of stature. Am. J. Med. Genet. 113 (2002) 29-39
14. Huang Q.Y., Xu F.H., Shen H., Deng H.Y., Conway T., Liu Y.J., Liu Y.Z., Li J.L., Li M.X., Davies K.M., Recker R.R., and Deng H.W. Genome scan for QTLs underlying bone size variation at 10 refined skeletal sites: genetic heterogeneity and the significance of phenotype refinement. Physiol. Genomics 17 (2004) 326-331
15. Li X., Masinde G., Gu W., Wergedal J., Mohan S., and Baylink D.J. Genetic dissection of femur breaking strength in a large population (MRL/MpJ × SJL/J) of F2 Mice: single QTL effects, epistasis, and pleiotropy. Genomics 79 (2002) 734-740
16. Li X., Masinde G., Gu W., Wergedal J., Hamilton-Ulland M., Xu S., Mohan S., and Baylink D.J. Chromosomal regions harboring genes for the work to femur failure in mice. Funct. Integr. Genomics 1 2002 (2002) 367-374
17. Klein R.F., Turner R.J., Skinner L.D., Vartanian K.A., Serang M., Carlos A.S., Shea M., Belknap J.K., and Orwoll E.S. Mapping quantitative trait loci that influence femoral cross-sectional area in mice. J. Bone Miner. Res. 17 (2002) 1752-1760
18. Alam I., Sun Q., Liu L., Koller D.L., Carr L.G., Econs M.J., Foroud T., and Turner C.H. Sex-specific genetic loci for femoral neck bone mass and strength identified in inbred COP and DA rats. J. Bone. Miner. Res. 23 (2008) 850-859
19. Sun Q., Alam I., Liu L., Koller D.L., Carr L.G., Econs M.J., Foroud T., and Turner C.H. Genetic loci affecting bone structure and strength in inbred COP and DA rats. Bone 42 (2008) 547-553
20. Alam I., Sun Q., Liu L., Koller D.L., Fishburn T., Carr L.G., Econs M.J., Foroud T., and Turner C.H. Whole-genome scan for linkage to bone strength and structure in inbred Fischer 344 and Lewis rats. J. Bone Miner. Res. 20 (2005) 1589-1596
21. Alam I., Sun Q., Liu L., Koller D.L., Fishburn T., Carr L.G., Econs M.J., Foroud T., and Turner C.H. Identification of a quantitative trait locus on rat chromosome 4 that is strongly linked to femoral neck structure and strength. Bone 39 (2006) 93-99
22. Turner C.H., Roeder R.K., Wieczorek A., Foroud T., Liu G., and Peacock M. Variability in skeletal mass, structure, and biomechanical properties among inbred strains of rats. J. Bone Miner. Res. 16 (2001) 1532-1539
23. Alam I., Sun Q., Liu L., Koller D.L., Liu L., Edenberg H.J., Econs M.J., Foroud T., and Turner C.H. Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck. Physiol. Genomics 35 (2008) 191-196
24. Smyth G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3 (2004) Article3
25. McClintick J.N., and Edenberg H.J. Effects of filtering by present call on analysis of microarray experiments. BMC. Bioinformatics 7 (2006) 49
26. Benjamini Y., and Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57 (1995) 289-290
27. Batut J., Schmierer B., Cao J., Raftery L.A., Hill C.S., and Howell M M. Two highly related regulatory subunits of PP2A exert opposite effects on TGF-beta/Activin/Nodal signaling. Development 135 (2008) 2927-2937
28. Stehlik C., Fiorentino L., Dorfleutner A., Bruey J.M., Ariza E.M., Sagara J., and Reed J.C. The PAAD/PYRIN-family protein ASC is a dual regulator of a conserved step in nuclear factor kappaB activation pathways. J. Exp. Med. 196 (2002) 1605-1615
29. Koller D.L., Econs M.J., Morin P.A., Christian J.C., Hui S.L., Parry P., Curran M.E., Rodriguez L.A., Conneally P.M., Joslyn G., Peacock M., Johnston C.C., and Foroud T. Genome screen for QTLs contributing to normal variation in bone mineral density and osteoporosis. J. Clin. Endocrinol. Metab. 85 (2000) 3116-3120
30. Takayanagi H., Sato K., Takaoka A., and Taniguchi T. Interplay between interferon and other cytokine systems in bone metabolism. Immunol. Rev. 208 (2005) 181-193
31. Gdynia G., Lehmann-Koch J., Sieber S., Tagscherer K.E., Fassl A., Zentgraf H., Matsuzawa S., Reed J.C., and Roth W. BLOC1S2 interacts with the HIPPI protein and sensitizes NCH89 glioblastoma cells to apoptosis. Apoptosis 13 (2008) 437-447
32. Ohno H. Physiological roles of clathrin adaptor AP complexes: lessons from mutant animals. J. Biochem. 139 (2006) 943-948
33. Blitzer J.T., and Nusse R. A critical role for endocytosis in Wnt signaling. BMC. Cell. Biol. 7 (2006) 28
34. Mizoguchi T., Nakajima K., Hatsuzawa K., Nagahama M., Hauri H.P., Tagaya M., and Tani K. Determination of functional regions of p125, a novel mammalian Sec23p-interacting protein. Biochem. Biophys. Res. Commun. 279 (2000) 144-149
35. Calvano S.E., Xiao W., Richards D.R., Felciano R.M., Baker H.V., Cho R.J., Chen R.O., Brownstein B.H., Cobb J.P., Tschoeke S.K., Miller-Graziano C., Moldawer L.L., Mindrinos M.N., Davis R.W., Tompkins R.G., and Lowry S.F. A network-based analysis of systemic inflammation in humans. Nature 437 (2005) 1032-1037
36. Li X., Liu H., Qin L., Tamasi J., Bergenstock M., Shapses S., Feyen J.H., Notterman D.A., and Partridge N.C. Determination of dual effects of parathyroid hormone on skeletal gene expression in vivo by microarray and network analysis. J. Biol. Chem. 282 (2007) 33086-33097
37. Lynch M.P., Capparelli C., Stein J.L., Stein G.S., and Lian J.B. Apoptosis during bone-like tissue development in vitro. J. Cell. Biochem. 68 (1998) 31-49
38. Takayanagi H., Kim S., Matsuo K., Suzuki H., Suzuki T., Sato K., Yokochi T., Oda H., Nakamura K., Ida N., Wagner E.F., and Taniguchi T. RANKL maintains bone homeostasis through c-Fos-dependent induction of interferon-beta. Nature 416 (2002) 744-749
39. Townley A.K., Feng Y., Schmidt K., Carter D.A., Porter R., Verkade P., and Stephens D.J. Efficient coupling of Sec23-Sec24 to Sec13-Sec31 drives COPII-dependent collagen secretion and is essential for normal craniofacial development. J. Cell. Sci. 121 (2008) 3025-3034
40. Kearns A.E., Khosla S., and Kostenuik P.J. Receptor activator of nuclear factor kappaB ligand and osteoprotegerin regulation of bone remodeling in health and disease. Endocr. Rev. 29 (2008) 155-192
41. Gingery A., Bradley E., Shaw A., and Oursler M.J. Phosphatidylinositol 3-kinase coordinately activates the MEK/ERK and AKT/NFkappaB pathways to maintain osteoclast survival. J. Cell. Biochem. 89 (2003) 165-179
42. Ge C., Xiao G., Jiang D., and Franceschi R.T. Critical role of the extracellular signal-regulated kinase-MAPK pathway in osteoblast differentiation and skeletal development. J. Cell. Biol. 176 (2007) 709-718
43. Lee S.E., Woo K.M., Kim S.Y., Kim H.M., Kwack K., Lee Z.H., and Kim H.H. The phosphatidylinositol 3-kinase, p38, and extracellular signal-regulated kinase pathways are involved in osteoclast differentiation. Bone 30 (2002) 71-77
44. Horowitz M.C., Xi Y., Wilson K., and Kacena M.A. Control of osteoclastogenesis and bone resorption by members of the TNF family of receptors and ligands. Cytokine. Growth. Factor. Rev. 12 (2001) 9-18