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Volumn 4, Issue 1, 2017, Pages 46-59.e4

Integrating GWAS and Co-expression Network Data Identifies Bone Mineral Density Genes SPTBN1 and MARK3 and an Osteoblast Functional Module

Author keywords

BMD; bone fragility; bone mineral density; co expression network; fracture; genetics; genome wide association study; GWAS; osteoporosis; systems genetics

Indexed keywords

MARK3 PROTEIN; MEMBRANE PROTEIN; SPTBN1 PROTEIN; UNCLASSIFIED DRUG; MARK3 PROTEIN, HUMAN; PROTEIN SERINE THREONINE KINASE; SPECTRIN; SPTBN1 PROTEIN, HUMAN; TRANSCRIPTOME;

EID: 85006746732     PISSN: 24054712     EISSN: 24054720     Source Type: Journal    
DOI: 10.1016/j.cels.2016.10.014     Document Type: Article
Times cited : (89)

References (70)
  • 4
    • 85001837234 scopus 로고    scopus 로고
    • Clinical practice. Postmenopausal osteoporosis
    • Black, D.M., Rosen, C.J., Clinical practice. Postmenopausal osteoporosis. N. Engl. J. Med. 374 (2016), 254–262.
    • (2016) N. Engl. J. Med. , vol.374 , pp. 254-262
    • Black, D.M.1    Rosen, C.J.2
  • 5
    • 79251493453 scopus 로고    scopus 로고
    • The amazing osteocyte
    • Bonewald, L.F., The amazing osteocyte. J. Bone Miner. Res. 26 (2011), 229–238.
    • (2011) J. Bone Miner. Res. , vol.26 , pp. 229-238
    • Bonewald, L.F.1
  • 6
    • 0037673945 scopus 로고    scopus 로고
    • Osteoclast differentiation and activation
    • Boyle, W.J., Simonet, W.S., Lacey, D.L., Osteoclast differentiation and activation. Nature 423 (2003), 337–342.
    • (2003) Nature , vol.423 , pp. 337-342
    • Boyle, W.J.1    Simonet, W.S.2    Lacey, D.L.3
  • 7
    • 63849210402 scopus 로고    scopus 로고
    • The regulation and function of mammalian AMPK-related kinases
    • Bright, N.J., Thornton, C., Carling, D., The regulation and function of mammalian AMPK-related kinases. Acta Physiol. (Oxf.) 196 (2009), 15–26.
    • (2009) Acta Physiol. (Oxf.) , vol.196 , pp. 15-26
    • Bright, N.J.1    Thornton, C.2    Carling, D.3
  • 8
    • 84867337003 scopus 로고    scopus 로고
    • The International Mouse Phenotyping Consortium: Past and future perspectives on mouse phenotyping
    • Brown, S.D.M., Moore, M.W., The International Mouse Phenotyping Consortium: Past and future perspectives on mouse phenotyping. Mamm. Genome 23 (2012), 632–640.
    • (2012) Mamm. Genome , vol.23 , pp. 632-640
    • Brown, S.D.M.1    Moore, M.W.2
  • 9
    • 84860743865 scopus 로고    scopus 로고
    • Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium
    • Brown, S.D.M., Moore, M.W., Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium. Dis. Model. Mech. 5 (2012), 289–292.
    • (2012) Dis. Model. Mech. , vol.5 , pp. 289-292
    • Brown, S.D.M.1    Moore, M.W.2
  • 12
    • 84864402194 scopus 로고    scopus 로고
    • Leveraging models of cell regulation and GWAS data in integrative network-based association studies
    • Califano, A., Butte, A.J., Friend, S., Ideker, T., Schadt, E., Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat. Genet. 44 (2012), 841–847.
    • (2012) Nat. Genet. , vol.44 , pp. 841-847
    • Califano, A.1    Butte, A.J.2    Friend, S.3    Ideker, T.4    Schadt, E.5
  • 16
    • 67349188883 scopus 로고    scopus 로고
    • A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits
    • Cho, Y.S., Go, M.J., Kim, Y.J., Heo, J.Y., Oh, J.H., Ban, H.-J., Yoon, D., Lee, M.H., Kim, D.-J., Park, M., et al. A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits. Nat. Genet. 41 (2009), 527–534.
    • (2009) Nat. Genet. , vol.41 , pp. 527-534
    • Cho, Y.S.1    Go, M.J.2    Kim, Y.J.3    Heo, J.Y.4    Oh, J.H.5    Ban, H.-J.6    Yoon, D.7    Lee, M.H.8    Kim, D.-J.9    Park, M.10
  • 19
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489 (2012), 57–74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 20
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • Ernst, J., Kellis, M., ChromHMM: Automating chromatin-state discovery and characterization. Nat. Methods 9 (2012), 215–216.
    • (2012) Nat. Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 22
    • 78349288821 scopus 로고    scopus 로고
    • Identification of a gene module associated with BMD through the integration of network analysis and genome-wide association data
    • Farber, C.R., Identification of a gene module associated with BMD through the integration of network analysis and genome-wide association data. J. Bone Miner. Res. 25 (2010), 2359–2367.
    • (2010) J. Bone Miner. Res. , vol.25 , pp. 2359-2367
    • Farber, C.R.1
  • 23
    • 84883141967 scopus 로고    scopus 로고
    • Systems-level analysis of genome-wide association data
    • Farber, C.R., Systems-level analysis of genome-wide association data. G3 (Bethesda) 3 (2013), 119–129.
    • (2013) G3 (Bethesda) , vol.3 , pp. 119-129
    • Farber, C.R.1
  • 25
    • 62549085618 scopus 로고    scopus 로고
    • Human genetic variation and its contribution to complex traits
    • Frazer, K.A., Murray, S.S., Schork, N.J., Topol, E.J., Human genetic variation and its contribution to complex traits. Nat. Rev. Genet. 10 (2009), 241–251.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 241-251
    • Frazer, K.A.1    Murray, S.S.2    Schork, N.J.3    Topol, E.J.4
  • 26
    • 33645059209 scopus 로고    scopus 로고
    • Preventing osteoporosis-related fractures: An overview
    • Gass, M., Dawson-Hughes, B., Preventing osteoporosis-related fractures: An overview. Am. J. Med. 119:4, Suppl 1 (2006), S3–S11.
    • (2006) Am. J. Med. , vol.119 , Issue.4 , pp. S3-S11
    • Gass, M.1    Dawson-Hughes, B.2
  • 31
    • 84884214071 scopus 로고    scopus 로고
    • An intact connexin43 is required to enhance signaling and gene expression in osteoblast-like cells
    • Hebert, C., Stains, J.P., An intact connexin43 is required to enhance signaling and gene expression in osteoblast-like cells. J. Cell. Biochem. 114 (2013), 2542–2550.
    • (2013) J. Cell. Biochem. , vol.114 , pp. 2542-2550
    • Hebert, C.1    Stains, J.P.2
  • 33
    • 84893174522 scopus 로고    scopus 로고
    • Network.assisted analysis to prioritize GWAS results: Principles, methods and perspectives
    • Jia, P., Zhao, Z., Network.assisted analysis to prioritize GWAS results: Principles, methods and perspectives. Hum. Genet. 133 (2014), 125–138.
    • (2014) Hum. Genet. , vol.133 , pp. 125-138
    • Jia, P.1    Zhao, Z.2
  • 34
    • 84903486426 scopus 로고    scopus 로고
    • Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment
    • Kemp, J.P., Medina-Gómez, C., Estrada, K., St Pourcain, B., Heppe, D.H.M., Warrington, N.M., Oei, L., Ring, S.M., Kruithof, C.J., Timpson, N.J., et al. Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment. PLoS Genet., 10, 2014, e1004423.
    • (2014) PLoS Genet. , vol.10 , pp. e1004423
    • Kemp, J.P.1    Medina-Gómez, C.2    Estrada, K.3    St Pourcain, B.4    Heppe, D.H.M.5    Warrington, N.M.6    Oei, L.7    Ring, S.M.8    Kruithof, C.J.9    Timpson, N.J.10
  • 36
    • 84940062348 scopus 로고    scopus 로고
    • PhenStat: A tool kit for standardized analysis of high throughput phenotypic data
    • Kurbatova, N., Mason, J.C., Morgan, H., Meehan, T.F., Karp, N.A., PhenStat: A tool kit for standardized analysis of high throughput phenotypic data. PLoS ONE, 10, 2015, e0131274.
    • (2015) PLoS ONE , vol.10 , pp. e0131274
    • Kurbatova, N.1    Mason, J.C.2    Morgan, H.3    Meehan, T.F.4    Karp, N.A.5
  • 39
    • 84956925118 scopus 로고    scopus 로고
    • Least-squares means: The R package lsmeans
    • Published online January 29, 2016
    • Lenth, R.V., Least-squares means: The R package lsmeans. J. Stat. Softw., 2016, 10.18637/jss.v069.i01 Published online January 29, 2016.
    • (2016) J. Stat. Softw.
    • Lenth, R.V.1
  • 42
    • 84863375739 scopus 로고    scopus 로고
    • Heritability of prevalent vertebral fracture and volumetric bone mineral density and geometry at the lumbar spine in three generations of the Framingham study
    • Liu, C.-T., Karasik, D., Zhou, Y., Hsu, Y.-H., Genant, H.K., Broe, K.E., Lang, T.F., Samelson, E.J., Demissie, S., Bouxsein, M.L., et al. Heritability of prevalent vertebral fracture and volumetric bone mineral density and geometry at the lumbar spine in three generations of the Framingham study. J. Bone Miner. Res. 27 (2012), 954–958.
    • (2012) J. Bone Miner. Res. , vol.27 , pp. 954-958
    • Liu, C.-T.1    Karasik, D.2    Zhou, Y.3    Hsu, Y.-H.4    Genant, H.K.5    Broe, K.E.6    Lang, T.F.7    Samelson, E.J.8    Demissie, S.9    Bouxsein, M.L.10
  • 43
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method
    • Livak, K.J., Schmittgen, T.D., Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25 (2001), 402–408.
    • (2001) Methods , vol.25 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2
  • 44
    • 84905491435 scopus 로고    scopus 로고
    • Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease
    • Mäkinen, V.-P., Civelek, M., Meng, Q., Zhang, B., Zhu, J., Levian, C., Huan, T., Segrè, A.V., Ghosh, S., Vivar, J., et al., Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Consortium. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PLoS Genet., 10, 2014, e1004502.
    • (2014) PLoS Genet. , vol.10 , pp. e1004502
    • Mäkinen, V.-P.1    Civelek, M.2    Meng, Q.3    Zhang, B.4    Zhu, J.5    Levian, C.6    Huan, T.7    Segrè, A.V.8    Ghosh, S.9    Vivar, J.10
  • 45
    • 84863897868 scopus 로고    scopus 로고
    • Meta-analysis of genome-wide scans for total body BMD in children and adults reveals allelic heterogeneity and age-specific effects at the WNT16 locus
    • Medina-Gómez, C., Kemp, J.P., Estrada, K., Eriksson, J., Liu, J., Reppe, S., Evans, D.M., Heppe, D.H.M., Vandenput, L., Herrera, L., et al. Meta-analysis of genome-wide scans for total body BMD in children and adults reveals allelic heterogeneity and age-specific effects at the WNT16 locus. PLoS Genet., 8, 2012, e1002718.
    • (2012) PLoS Genet. , vol.8 , pp. e1002718
    • Medina-Gómez, C.1    Kemp, J.P.2    Estrada, K.3    Eriksson, J.4    Liu, J.5    Reppe, S.6    Evans, D.M.7    Heppe, D.H.M.8    Vandenput, L.9    Herrera, L.10
  • 48
    • 0037059614 scopus 로고    scopus 로고
    • The novel zinc finger-containing transcription factor osterix is required for osteoblast differentiation and bone formation
    • Nakashima, K., Zhou, X., Kunkel, G., Zhang, Z., Deng, J.M., Behringer, R.R., de Crombrugghe, B., The novel zinc finger-containing transcription factor osterix is required for osteoblast differentiation and bone formation. Cell 108 (2002), 17–29.
    • (2002) Cell , vol.108 , pp. 17-29
    • Nakashima, K.1    Zhou, X.2    Kunkel, G.3    Zhang, Z.4    Deng, J.M.5    Behringer, R.R.6    de Crombrugghe, B.7
  • 49
    • 70350731110 scopus 로고    scopus 로고
    • Coexpression network based on natural variation in human gene expression reveals gene interactions and functions
    • Nayak, R.R., Kearns, M., Spielman, R.S., Cheung, V.G., Coexpression network based on natural variation in human gene expression reveals gene interactions and functions. Genome Res. 19 (2009), 1953–1962.
    • (2009) Genome Res. , vol.19 , pp. 1953-1962
    • Nayak, R.R.1    Kearns, M.2    Spielman, R.S.3    Cheung, V.G.4
  • 51
    • 23644456550 scopus 로고    scopus 로고
    • The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans
    • Ozanick, S., Krecic, A., Andersland, J., Anderson, J.T., The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. RNA 11 (2005), 1281–1290.
    • (2005) RNA , vol.11 , pp. 1281-1290
    • Ozanick, S.1    Krecic, A.2    Andersland, J.3    Anderson, J.T.4
  • 52
    • 84964927929 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • R Foundation for Statistical Computing
    • R Core Development Team. R: A language and environment for statistical computing. 2015, R Foundation for Statistical Computing.
    • (2015)
  • 53
    • 33748680524 scopus 로고    scopus 로고
    • Genetic regulation of bone mass and susceptibility to osteoporosis
    • Ralston, S.H., de Crombrugghe, B., Genetic regulation of bone mass and susceptibility to osteoporosis. Genes Dev. 20 (2006), 2492–2506.
    • (2006) Genes Dev. , vol.20 , pp. 2492-2506
    • Ralston, S.H.1    de Crombrugghe, B.2
  • 56
    • 84863205849 scopus 로고    scopus 로고
    • NIH Image to ImageJ: 25 years of image analysis
    • Schneider, C.A., Rasband, W.S., Eliceiri, K.W., NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9 (2012), 671–675.
    • (2012) Nat. Methods , vol.9 , pp. 671-675
    • Schneider, C.A.1    Rasband, W.S.2    Eliceiri, K.W.3
  • 57
  • 63
    • 0030042322 scopus 로고    scopus 로고
    • Spectrin: On the path from structure to function
    • Viel, A., Branton, D., Spectrin: On the path from structure to function. Curr. Opin. Cell Biol. 8 (1996), 49–55.
    • (1996) Curr. Opin. Cell Biol. , vol.8 , pp. 49-55
    • Viel, A.1    Branton, D.2
  • 64
    • 85151937310 scopus 로고    scopus 로고
    • Linear Mixed Models: A Practical Guide Using Statistical Software
    • CRC Press
    • West, B.T., Welch, K.B., Galecki, A.T., Linear Mixed Models: A Practical Guide Using Statistical Software. 2014, CRC Press.
    • (2014)
    • West, B.T.1    Welch, K.B.2    Galecki, A.T.3
  • 66
    • 23944458138 scopus 로고    scopus 로고
    • A general framework for weighted gene co-expression network analysis
    • Published online August 12, 2005
    • Zhang, B., Horvath, S., A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol., 4, 2005, Article17 Published online August 12, 2005.
    • (2005) Stat. Appl. Genet. Mol. Biol. , vol.4 , pp. Article17
    • Zhang, B.1    Horvath, S.2
  • 68
    • 84889675736 scopus 로고    scopus 로고
    • Spectrin: Structure, function and disease
    • Zhang, R., Zhang, C., Zhao, Q., Li, D., Spectrin: Structure, function and disease. Sci. China Life Sci. 56 (2013), 1076–1085.
    • (2013) Sci. China Life Sci. , vol.56 , pp. 1076-1085
    • Zhang, R.1    Zhang, C.2    Zhao, Q.3    Li, D.4
  • 69
    • 84856402164 scopus 로고    scopus 로고
    • Insights into the genetics of osteoporosis from recent genome-wide association studies
    • Zheng, H.-F., Spector, T.D., Richards, J.B., Insights into the genetics of osteoporosis from recent genome-wide association studies. Expert Rev. Mol. Med., 13, 2011, e28.
    • (2011) Expert Rev. Mol. Med. , vol.13 , pp. e28
    • Zheng, H.-F.1    Spector, T.D.2    Richards, J.B.3


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