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Volumn 8, Issue 1, 2016, Pages

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; SCLEROPROTEIN; TRANSFORMING GROWTH FACTOR BETA;

EID: 84961664673     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-016-0285-0     Document Type: Article
Times cited : (62)

References (115)
  • 2
    • 35948954244 scopus 로고    scopus 로고
    • Hepatic stellate cells: protean, multifunctional, and enigmatic cells of the liver
    • Friedman SL. Hepatic stellate cells: protean, multifunctional, and enigmatic cells of the liver. Physiol Rev. 2008;88:125-72.
    • (2008) Physiol Rev. , vol.88 , pp. 125-172
    • Friedman, S.L.1
  • 3
    • 0041897219 scopus 로고
    • Increase in type I and type III collagens in human alcoholic liver cirrhosis
    • Rojkind M, Martinez-Palomo A. Increase in type I and type III collagens in human alcoholic liver cirrhosis. Proc Natl Acad Sci U S A. 1976;73:539-43.
    • (1976) Proc Natl Acad Sci U S A. , vol.73 , pp. 539-543
    • Rojkind, M.1    Martinez-Palomo, A.2
  • 5
    • 0022632409 scopus 로고
    • Cell types involved in collagen and fibronectin production in normal and fibrotic human liver
    • Clement B, Grimaud J-A, Campion J-P, Deugnier Y, Guillouzo A. Cell types involved in collagen and fibronectin production in normal and fibrotic human liver. Hepatology. 1986;6:225-34.
    • (1986) Hepatology. , vol.6 , pp. 225-234
    • Clement, B.1    Grimaud, J.-A.2    Campion, J.-P.3    Deugnier, Y.4    Guillouzo, A.5
  • 6
    • 0018892253 scopus 로고
    • Distribution of basement membrane proteins in normal and fibrotic human liver: collagen type IV, laminin, and fibronectin
    • Hahn E, Wick G, Pencev D, Timpl R. Distribution of basement membrane proteins in normal and fibrotic human liver: collagen type IV, laminin, and fibronectin. Gut. 1980;21:63-71.
    • (1980) Gut. , vol.21 , pp. 63-71
    • Hahn, E.1    Wick, G.2    Pencev, D.3    Timpl, R.4
  • 7
    • 0028953768 scopus 로고
    • Hepatic expression of mature transforming growth factor beta 1 in transgenic mice results in multiple tissue lesions
    • Sanderson N, Factor V, Nagy P, Kopp J, Kondaiah P, Wakefield L, et al. Hepatic expression of mature transforming growth factor beta 1 in transgenic mice results in multiple tissue lesions. Proc Natl Acad Sci U S A. 1995;92:2572-6.
    • (1995) Proc Natl Acad Sci U S A. , vol.92 , pp. 2572-2576
    • Sanderson, N.1    Factor, V.2    Nagy, P.3    Kopp, J.4    Kondaiah, P.5    Wakefield, L.6
  • 8
    • 0031454239 scopus 로고    scopus 로고
    • Hepatic fibrosis, glomerulosclerosis, and a lipodystrophy-like syndrome in PEPCK-TGF-beta1 transgenic mice
    • Clouthier DE, Comerford SA, Hammer RE. Hepatic fibrosis, glomerulosclerosis, and a lipodystrophy-like syndrome in PEPCK-TGF-beta1 transgenic mice. J Clin Invest. 1997;100:2697-713.
    • (1997) J Clin Invest. , vol.100 , pp. 2697-2713
    • Clouthier, D.E.1    Comerford, S.A.2    Hammer, R.E.3
  • 9
  • 10
    • 84888339170 scopus 로고    scopus 로고
    • Fate tracing reveals hepatic stellate cells as dominant contributors to liver fibrosis independent of its aetiology
    • Mederacke I, Hsu CC, Troeger JS, Huebener P, Mu X, Dapito DH, et al. Fate tracing reveals hepatic stellate cells as dominant contributors to liver fibrosis independent of its aetiology. Nat Commun. 2013;4:2823.
    • (2013) Nat Commun. , vol.4 , pp. 2823
    • Mederacke, I.1    Hsu, C.C.2    Troeger, J.S.3    Huebener, P.4    Mu, X.5    Dapito, D.H.6
  • 11
    • 0026537533 scopus 로고
    • Isolated hepatic lipocytes and Kupffer cells from normal human liver: morphological and functional characteristics in primary culture
    • Friedman SL, Rockey DC, McGuire RF, Maher JJ, Boyles JK, Yamasaki G. Isolated hepatic lipocytes and Kupffer cells from normal human liver: morphological and functional characteristics in primary culture. Hepatology. 1992;15:234-43.
    • (1992) Hepatology. , vol.15 , pp. 234-243
    • Friedman, S.L.1    Rockey, D.C.2    McGuire, R.F.3    Maher, J.J.4    Boyles, J.K.5    Yamasaki, G.6
  • 12
    • 24344500807 scopus 로고    scopus 로고
    • Smad2 and Smad3 play different roles in rat hepatic stellate cell function and alpha-smooth muscle actin organization
    • Uemura M, Swenson ES, Gaça MDA, Giordano FJ, Reiss M, Wells RG. Smad2 and Smad3 play different roles in rat hepatic stellate cell function and alpha-smooth muscle actin organization. Mol Biol Cell. 2005;16:4214-24.
    • (2005) Mol Biol Cell. , vol.16 , pp. 4214-4224
    • Uemura, M.1    Swenson, E.S.2    Gaça, M.D.A.3    Giordano, F.J.4    Reiss, M.5    Wells, R.G.6
  • 14
  • 17
    • 0038374866 scopus 로고    scopus 로고
    • Conditional tetracycline-regulated expression of TGF-beta1 in liver of transgenic mice leads to reversible intermediary fibrosis
    • Ueberham E, Löw R, Ueberham U, Schönig K, Bujard H, Gebhardt R. Conditional tetracycline-regulated expression of TGF-beta1 in liver of transgenic mice leads to reversible intermediary fibrosis. Hepatology. 2003;37:1067-78.
    • (2003) Hepatology. , vol.37 , pp. 1067-1078
    • Ueberham, E.1    Löw, R.2    Ueberham, U.3    Schönig, K.4    Bujard, H.5    Gebhardt, R.6
  • 18
    • 0025821563 scopus 로고
    • Modulation of alpha smooth muscle actin and desmin expression in perisinusoidal cells of normal and diseased human livers
    • Schmitt-Gräff A, Krüger S, Bochard F, Gabbiani G, Denk H. Modulation of alpha smooth muscle actin and desmin expression in perisinusoidal cells of normal and diseased human livers. Am J Pathol. 1991;138:1233-42.
    • (1991) Am J Pathol. , vol.138 , pp. 1233-1242
    • Schmitt-Gräff, A.1    Krüger, S.2    Bochard, F.3    Gabbiani, G.4    Denk, H.5
  • 19
    • 0026846805 scopus 로고
    • Rat hepatic lipocytes express smooth muscle actin upon activation in vivo and in culture
    • Rockey DC, Boyles JK, Gabbiani G, Friedman SL. Rat hepatic lipocytes express smooth muscle actin upon activation in vivo and in culture. J Submicrosc Cytol Pathol. 1992;24:193-203.
    • (1992) J Submicrosc Cytol Pathol. , vol.24 , pp. 193-203
    • Rockey, D.C.1    Boyles, J.K.2    Gabbiani, G.3    Friedman, S.L.4
  • 20
    • 84878235678 scopus 로고    scopus 로고
    • Hepatic stellate cells and portal fibroblasts are the major cellular sources of collagens and lysyl oxidases in normal liver and early after injury
    • Perepelyuk M, Terajima M, Wang AY, Georges PC, Janmey PA, Yamauchi M, et al. Hepatic stellate cells and portal fibroblasts are the major cellular sources of collagens and lysyl oxidases in normal liver and early after injury. Am J Physiol Gastrointest Liver Physiol. 2013;304:G605-14.
    • (2013) Am J Physiol Gastrointest Liver Physiol. , vol.304 , pp. G605-G614
    • Perepelyuk, M.1    Terajima, M.2    Wang, A.Y.3    Georges, P.C.4    Janmey, P.A.5    Yamauchi, M.6
  • 21
    • 84892622834 scopus 로고    scopus 로고
    • Reversibility of liver fibrosis and inactivation of fibrogenic myofibroblasts
    • Liu X, Xu J, Brenner DA, Kisseleva T. Reversibility of liver fibrosis and inactivation of fibrogenic myofibroblasts. Curr Pathobiol Rep. 2013;1:209-14.
    • (2013) Curr Pathobiol Rep. , vol.1 , pp. 209-214
    • Liu, X.1    Xu, J.2    Brenner, D.A.3    Kisseleva, T.4
  • 23
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012;81:145-66.
    • (2012) Annu Rev Biochem. , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 24
    • 84891798006 scopus 로고    scopus 로고
    • NONCODEv4: exploring the world of long non-coding RNA genes
    • Xie C, Yuan J, Li H, Li M, Zhao G, Bu D, et al. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res. 2014;42(Database issue):D98-103.
    • (2014) Nucleic Acids Res , vol.42 , Issue.DATABASE ISSUE , pp. D98-103
    • Xie, C.1    Yuan, J.2    Li, H.3    Li, M.4    Zhao, G.5    Bu, D.6
  • 26
    • 55349109963 scopus 로고    scopus 로고
    • Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome
    • Zhao J, Sun BK, Erwin JA, Song J-J, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science. 2008;322:750-6.
    • (2008) Science. , vol.322 , pp. 750-756
    • Zhao, J.1    Sun, B.K.2    Erwin, J.A.3    Song, J.-J.4    Lee, J.T.5
  • 27
    • 67650921949 scopus 로고    scopus 로고
    • Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    • Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009;106:11667-72.
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , pp. 11667-11672
    • Khalil, A.M.1    Guttman, M.2    Huarte, M.3    Garber, M.4    Raj, A.5    Rivea Morales, D.6
  • 28
    • 84872135457 scopus 로고    scopus 로고
    • Control of somatic tissue differentiation by the long non-coding RNA TINCR
    • Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013;493:231-5.
    • (2013) Nature. , vol.493 , pp. 231-235
    • Kretz, M.1    Siprashvili, Z.2    Chu, C.3    Webster, D.E.4    Zehnder, A.5    Qu, K.6
  • 30
    • 84899486799 scopus 로고    scopus 로고
    • The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation
    • Wang P, Xue Y, Han Y, Lin L, Wu C, Xu S, et al. The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science. 2014;344:310-3.
    • (2014) Science. , vol.344 , pp. 310-313
    • Wang, P.1    Xue, Y.2    Han, Y.3    Lin, L.4    Wu, C.5    Xu, S.6
  • 31
    • 84885740857 scopus 로고    scopus 로고
    • Targeted disruption of Hotair leads to homeotic transformation and gene derepression
    • Li L, Liu B, Wapinski OL, Tsai M-C, Qu K, Zhang J, et al. Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep. 2013;5:3-12.
    • (2013) Cell Rep. , vol.5 , pp. 3-12
    • Li, L.1    Liu, B.2    Wapinski, O.L.3    Tsai, M.-C.4    Qu, K.5    Zhang, J.6
  • 32
    • 84891757415 scopus 로고    scopus 로고
    • Multiple knockout mouse models reveal lincRNAs are required for life and brain development
    • Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2013;2:1-24.
    • (2013) Elife. , vol.2 , pp. 1-24
    • Sauvageau, M.1    Goff, L.A.2    Lodato, S.3    Bonev, B.4    Groff, A.F.5    Gerhardinger, C.6
  • 34
    • 84902437938 scopus 로고    scopus 로고
    • Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development
    • Herriges MJ, Swarr DT, Morley MP, Rathi KS, Peng T, Stewart KM, et al. Long noncoding RNAs are spatially correlated with transcription factors and regulate lung development. Genes Dev. 2014;28:1363-79.
    • (2014) Genes Dev. , vol.28 , pp. 1363-1379
    • Herriges, M.J.1    Swarr, D.T.2    Morley, M.P.3    Rathi, K.S.4    Peng, T.5    Stewart, K.M.6
  • 35
    • 84881478367 scopus 로고    scopus 로고
    • A long noncoding RNA mediates both activation and repression of immune response genes
    • Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science. 2013;341:789-92.
    • (2013) Science. , vol.341 , pp. 789-792
    • Carpenter, S.1    Aiello, D.2    Atianand, M.K.3    Ricci, E.P.4    Gandhi, P.5    Hall, L.L.6
  • 36
    • 84908020927 scopus 로고    scopus 로고
    • A long noncoding RNA protects the heart from pathological hypertrophy
    • Han P, Li W, Lin C-H, Yang J, Shang C, Nuernberg ST, et al. A long noncoding RNA protects the heart from pathological hypertrophy. Nature. 2014;514:102-6.
    • (2014) Nature , vol.514 , pp. 102-106
    • Han, P.1    Li, W.2    Lin, C.-H.3    Yang, J.4    Shang, C.5    Nuernberg, S.T.6
  • 37
    • 84880154515 scopus 로고    scopus 로고
    • Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer
    • Du Z, Fei T, Verhaak RGW, Su Z, Zhang Y, Brown M, et al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol. 2013;20:908-13.
    • (2013) Nat Struct Mol Biol. , vol.20 , pp. 908-913
    • Du, Z.1    Fei, T.2    Verhaak, R.G.W.3    Su, Z.4    Zhang, Y.5    Brown, M.6
  • 38
    • 70149123708 scopus 로고    scopus 로고
    • Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
    • Ponjavic J, Oliver PL, Lunter G, Ponting CP. Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet. 2009;5:e1000617.
    • (2009) PLoS Genet. , vol.5 , pp. e1000617
    • Ponjavic, J.1    Oliver, P.L.2    Lunter, G.3    Ponting, C.P.4
  • 39
    • 33846223294 scopus 로고    scopus 로고
    • Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA
    • Panzitt K, Tschernatsch MMO, Guelly C, Moustafa T, Stradner M, Strohmaier HM, et al. Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology. 2007;132:330-42.
    • (2007) Gastroenterology. , vol.132 , pp. 330-342
    • Panzitt, K.1    Tschernatsch, M.M.O.2    Guelly, C.3    Moustafa, T.4    Stradner, M.5    Strohmaier, H.M.6
  • 40
    • 33846950027 scopus 로고    scopus 로고
    • A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas
    • Lin R, Maeda S, Liu C, Karin M, Edgington TS. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene. 2007;26:851-8.
    • (2007) Oncogene. , vol.26 , pp. 851-858
    • Lin, R.1    Maeda, S.2    Liu, C.3    Karin, M.4    Edgington, T.S.5
  • 41
    • 79551674253 scopus 로고    scopus 로고
    • Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma
    • Braconi C, Valeri N, Kogure T, Gasparini P, Huang N, Nuovo GJ, et al. Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma. Proc Natl Acad Sci U S A. 2011;108:786-91.
    • (2011) Proc Natl Acad Sci U S A. , vol.108 , pp. 786-791
    • Braconi, C.1    Valeri, N.2    Kogure, T.3    Gasparini, P.4    Huang, N.5    Nuovo, G.J.6
  • 42
    • 80055046798 scopus 로고    scopus 로고
    • Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans
    • Yang F, Zhang L, Huo X, Yuan J, Xu D, Yuan S, et al. Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans. Hepatology. 2011;54:1679-89.
    • (2011) Hepatology. , vol.54 , pp. 1679-1689
    • Yang, F.1    Zhang, L.2    Huo, X.3    Yuan, J.4    Xu, D.5    Yuan, S.6
  • 43
    • 79955836034 scopus 로고    scopus 로고
    • Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation
    • Yang Z, Zhou L, Wu L-M, Lai M-C, Xie H-Y, Zhang F, et al. Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann Surg Oncol. 2011;18:1243-50.
    • (2011) Ann Surg Oncol. , vol.18 , pp. 1243-1250
    • Yang, Z.1    Zhou, L.2    Wu, L.-M.3    Lai, M.-C.4    Xie, H.-Y.5    Zhang, F.6
  • 44
    • 84870530823 scopus 로고    scopus 로고
    • Long noncoding RNA associated with microvascular invasion in hepatocellular carcinoma promotes angiogenesis and serves as a predictor for hepatocellular carcinoma patients' poor recurrence-free survival after hepatectomy
    • Yuan S-X, Yang F, Yang Y, Tao Q-F, Zhang J, Huang G, et al. Long noncoding RNA associated with microvascular invasion in hepatocellular carcinoma promotes angiogenesis and serves as a predictor for hepatocellular carcinoma patients' poor recurrence-free survival after hepatectomy. Hepatology. 2012;56:2231-41.
    • (2012) Hepatology. , vol.56 , pp. 2231-2241
    • Yuan, S.-X.1    Yang, F.2    Yang, Y.3    Tao, Q.-F.4    Zhang, J.5    Huang, G.6
  • 45
    • 84897438456 scopus 로고    scopus 로고
    • Modulation of hypoxia-signaling pathways by extracellular linc-RoR
    • Takahashi K, Yan IK, Haga H, Patel T. Modulation of hypoxia-signaling pathways by extracellular linc-RoR. J Cell Sci. 2014;127:1585-94.
    • (2014) J Cell Sci , vol.127 , pp. 1585-1594
    • Takahashi, K.1    Yan, I.K.2    Haga, H.3    Patel, T.4
  • 46
    • 84896710254 scopus 로고    scopus 로고
    • Long noncoding RNA HOTTIP/HOXA13 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients
    • Quagliata L, Matter MS, Piscuoglio S, Arabi L, Ruiz C, Procino A, et al. Long noncoding RNA HOTTIP/HOXA13 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients. Hepatology. 2014;59:911-23.
    • (2014) Hepatology. , vol.59 , pp. 911-923
    • Quagliata, L.1    Matter, M.S.2    Piscuoglio, S.3    Arabi, L.4    Ruiz, C.5    Procino, A.6
  • 47
    • 84927692286 scopus 로고    scopus 로고
    • Long non-coding RNA HOTTIP is frequently up-regulated in hepatocellular carcinoma and is targeted by tumour suppressive miR-125b
    • Tsang FHC, Au SLK, Wei L, Fan DNY, Lee JMF, Wong CCL, et al. Long non-coding RNA HOTTIP is frequently up-regulated in hepatocellular carcinoma and is targeted by tumour suppressive miR-125b. Liver Int. 2015;35:1597-606.
    • (2015) Liver Int , vol.35 , pp. 1597-1606
    • Tsang, F.H.C.1    Au, S.L.K.2    Wei, L.3    Fan, D.N.Y.4    Lee, J.M.F.5    Wong, C.C.L.6
  • 48
    • 84904795250 scopus 로고    scopus 로고
    • Epigenetics in liver disease
    • Mann DA. Epigenetics in liver disease. Hepatology. 2014;60:1418-25.
    • (2014) Hepatology. , vol.60 , pp. 1418-1425
    • Mann, D.A.1
  • 49
    • 84872825450 scopus 로고    scopus 로고
    • Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation
    • Lai M, Yang Z, Zhou L, Zhu Q, Xie H, Zhang F, et al. Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation. Med Oncol. 2012;29:1810-6.
    • (2012) Med Oncol. , vol.29 , pp. 1810-1816
    • Lai, M.1    Yang, Z.2    Zhou, L.3    Zhu, Q.4    Xie, H.5    Zhang, F.6
  • 50
    • 84887441210 scopus 로고    scopus 로고
    • Extracellular vesicle-mediated transfer of a novel long noncoding RNA TUC339: a mechanism of intercellular signaling in human hepatocellular cancer
    • Kogure T, Yan IK, Lin W-L, Patel T. Extracellular vesicle-mediated transfer of a novel long noncoding RNA TUC339: a mechanism of intercellular signaling in human hepatocellular cancer. Genes Cancer. 2013;4:261-72.
    • (2013) Genes Cancer. , vol.4 , pp. 261-272
    • Kogure, T.1    Yan, I.K.2    Lin, W.-L.3    Patel, T.4
  • 51
    • 84881027023 scopus 로고    scopus 로고
    • Long noncoding RNAs associated with liver regeneration 1 accelerates hepatocyte proliferation during liver regeneration by activating Wnt/β-catenin signaling
    • Xu D, Yang F, Yuan J, Zhang L, Bi H, Zhou C, et al. Long noncoding RNAs associated with liver regeneration 1 accelerates hepatocyte proliferation during liver regeneration by activating Wnt/β-catenin signaling. Hepatology. 2013;58:739-51.
    • (2013) Hepatology. , vol.58 , pp. 739-751
    • Xu, D.1    Yang, F.2    Yuan, J.3    Zhang, L.4    Bi, H.5    Zhou, C.6
  • 52
    • 84908053101 scopus 로고    scopus 로고
    • Inhibitory effects of long noncoding RNA MEG3 on hepatic stellate cells activation and liver fibrogenesis
    • He Y, Wu Y-T, Huang C, Meng X-M, Ma T-T, Wu B-M, et al. Inhibitory effects of long noncoding RNA MEG3 on hepatic stellate cells activation and liver fibrogenesis. Biochim Biophys Acta. 2014;1842(11):2204-15.
    • (2014) Biochim Biophys Acta , vol.1842 , Issue.11 , pp. 2204-2215
    • He, Y.1    Wu, Y.-T.2    Huang, C.3    Meng, X.-M.4    Ma, T.-T.5    Wu, B.-M.6
  • 53
    • 84947776036 scopus 로고    scopus 로고
    • Long non-coding RNA growth arrest-specific transcript 5 (GAS5) inhibits liver fibrogenesis through a mechanism of competing endogenous RNA
    • Yu F, Zheng J, Mao Y, Dong P, Lu Z, Li G, et al. Long non-coding RNA growth arrest-specific transcript 5 (GAS5) inhibits liver fibrogenesis through a mechanism of competing endogenous RNA. J Biol Chem. 2015;290:28286-98.
    • (2015) J Biol Chem. , vol.290 , pp. 28286-28298
    • Yu, F.1    Zheng, J.2    Mao, Y.3    Dong, P.4    Lu, Z.5    Li, G.6
  • 54
    • 81855183267 scopus 로고    scopus 로고
    • microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer
    • Braconi C, Kogure T, Valeri N, Huang N, Nuovo G, Costinean S, et al. microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene. 2011;30:4750-6.
    • (2011) Oncogene , vol.30 , pp. 4750-4756
    • Braconi, C.1    Kogure, T.2    Valeri, N.3    Huang, N.4    Nuovo, G.5    Costinean, S.6
  • 55
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25:1915-27.
    • (2011) Genes Dev. , vol.25 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3    Koziol, M.4    Tazon-Vega, B.5    Regev, A.6
  • 56
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    • Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22:1775-89.
    • (2012) Genome Res. , vol.22 , pp. 1775-1789
    • Derrien, T.1    Johnson, R.2    Bussotti, G.3    Tanzer, A.4    Djebali, S.5    Tilgner, H.6
  • 57
    • 84879671055 scopus 로고    scopus 로고
    • Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs
    • Hangauer MJ, Vaughn IW, McManus MT. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet. 2013;9:e1003569.
    • (2013) PLoS Genet. , vol.9 , pp. e1003569
    • Hangauer, M.J.1    Vaughn, I.W.2    McManus, M.T.3
  • 59
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-11.
    • (2009) Bioinformatics. , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 60
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562-78.
    • (2012) Nat Protoc. , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6
  • 61
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511-5.
    • (2010) Nat Biotechnol. , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Baren, M.J.6
  • 62
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 2010;28:503-10.
    • (2010) Nat Biotechnol. , vol.28 , pp. 503-510
    • Guttman, M.1    Garber, M.2    Levin, J.Z.3    Donaghey, J.4    Robinson, J.5    Adiconis, X.6
  • 64
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009;23:205-11.
    • (2009) Genome Inform. , vol.23 , pp. 205-211
    • Eddy, S.R.1
  • 65
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: interactive sequence similarity searching
    • Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39(Web Server issue):W29-37.
    • (2011) Nucleic Acids Res , vol.39 , Issue.WEB SERVER ISSUE , pp. W29-37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 66
    • 84876020023 scopus 로고    scopus 로고
    • CPAT: Coding-potential assessment tool using an alignment-free logistic regression model
    • Wang L, Park HJ, Dasari S, Wang S, Kocher J-P, Li W. CPAT: Coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013;41:e74.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e74
    • Wang, L.1    Park, H.J.2    Dasari, S.3    Wang, S.4    Kocher, J.-P.5    Li, W.6
  • 68
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357-9.
    • (2012) Nat Methods. , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 70
    • 84876216563 scopus 로고    scopus 로고
    • Master transcription factors and mediator establish super-enhancers at key cell identity genes
    • Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013;153:307-19.
    • (2013) Cell. , vol.153 , pp. 307-319
    • Whyte, W.A.1    Orlando, D.A.2    Hnisz, D.3    Abraham, B.J.4    Lin, C.Y.5    Kagey, M.H.6
  • 73
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq--a Python framework to work with high-throughput sequencing data
    • Anders S, Pyl PT, Huber W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014;31:166-9.
    • (2014) Bioinformatics. , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 74
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 76
    • 84855896819 scopus 로고    scopus 로고
    • Using MCL to extract clusters from networks
    • van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. Methods Mol Biol. 2012;804:281-95.
    • (2012) Methods Mol Biol. , vol.804 , pp. 281-295
    • Dongen, S.1    Abreu-Goodger, C.2
  • 77
  • 78
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44-57.
    • (2009) Nat Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 80
    • 84902286789 scopus 로고    scopus 로고
    • Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes
    • IIott NE, Heward JA, Roux B, Tsitsiou E, Fenwick PS, Lenzi L, et al. Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nat Commun. 2014;5:3979.
    • (2014) Nat Commun. , vol.5 , pp. 3979
    • IIott, N.E.1    Heward, J.A.2    Roux, B.3    Tsitsiou, E.4    Fenwick, P.S.5    Lenzi, L.6
  • 81
    • 0024314801 scopus 로고
    • Maintenance of differentiated phenotype of cultured rat hepatic lipocytes by basement membrane matrix
    • Friedman SL, Roll FJ, Boyles J, Arenson DM, Bissell DM. Maintenance of differentiated phenotype of cultured rat hepatic lipocytes by basement membrane matrix. J Biol Chem. 1989;264:10756-62.
    • (1989) J Biol Chem. , vol.264 , pp. 10756-10762
    • Friedman, S.L.1    Roll, F.J.2    Boyles, J.3    Arenson, D.M.4    Bissell, D.M.5
  • 82
    • 0036022840 scopus 로고    scopus 로고
    • Reversal of activation of human myofibroblast-like cells by culture on a basement membrane-like substrate
    • Sohara N, Znoyko I, Levy MT, Trojanowska M, Reuben A. Reversal of activation of human myofibroblast-like cells by culture on a basement membrane-like substrate. J Hepatol. 2002;37:214-21.
    • (2002) J Hepatol. , vol.37 , pp. 214-221
    • Sohara, N.1    Znoyko, I.2    Levy, M.T.3    Trojanowska, M.4    Reuben, A.5
  • 83
    • 84883496216 scopus 로고    scopus 로고
    • Predicting long non-coding RNAs using RNA sequencing
    • Ilott NE, Ponting CP. Predicting long non-coding RNAs using RNA sequencing. Methods. 2013;63:50-9.
    • (2013) Methods. , vol.63 , pp. 50-59
    • Ilott, N.E.1    Ponting, C.P.2
  • 86
    • 34447098370 scopus 로고    scopus 로고
    • A chromatin landmark and transcription initiation at most promoters in human cells
    • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell. 2007;130:77-88.
    • (2007) Cell. , vol.130 , pp. 77-88
    • Guenther, M.G.1    Levine, S.S.2    Boyer, L.A.3    Jaenisch, R.4    Young, R.A.5
  • 88
    • 84857836107 scopus 로고    scopus 로고
    • Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    • Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, et al. Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 2012;22:577-91.
    • (2012) Genome Res. , vol.22 , pp. 577-591
    • Pauli, A.1    Valen, E.2    Lin, M.F.3    Garber, M.4    Vastenhouw, N.L.5    Levin, J.Z.6
  • 90
    • 84876928036 scopus 로고    scopus 로고
    • A vitamin D receptor/SMAD genomic circuit gates hepatic fibrotic response
    • Ding N, Yu RT, Subramaniam N, Sherman MH, Wilson C, Rao R, et al. A vitamin D receptor/SMAD genomic circuit gates hepatic fibrotic response. Cell. 2013;153:601-13.
    • (2013) Cell. , vol.153 , pp. 601-613
    • Ding, N.1    Yu, R.T.2    Subramaniam, N.3    Sherman, M.H.4    Wilson, C.5    Rao, R.6
  • 91
    • 80155137594 scopus 로고    scopus 로고
    • Master transcription factors determine cell-type-specific responses to TGF-β signaling
    • Mullen AC, Orlando DA, Newman JJ, Lovén J, Kumar RM, Bilodeau S, et al. Master transcription factors determine cell-type-specific responses to TGF-β signaling. Cell. 2011;147:565-76.
    • (2011) Cell. , vol.147 , pp. 565-576
    • Mullen, A.C.1    Orlando, D.A.2    Newman, J.J.3    Lovén, J.4    Kumar, R.M.5    Bilodeau, S.6
  • 92
    • 79955550445 scopus 로고    scopus 로고
    • A user's guide to the encyclopedia of DNA elements (ENCODE)
    • Consortium TEP. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011;9:e1001046.
    • (2011) PLoS Biol. , vol.9 , pp. e1001046
    • Consortium, T.E.P.1
  • 93
    • 38549168494 scopus 로고    scopus 로고
    • Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory
    • Luo F, Yang Y, Zhong J, Gao H, Khan L, Thompson DK, et al. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics. 2007;8:299.
    • (2007) BMC Bioinformatics. , vol.8 , pp. 299
    • Luo, F.1    Yang, Y.2    Zhong, J.3    Gao, H.4    Khan, L.5    Thompson, D.K.6
  • 94
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol Syst Biol. 2007;3:88.
    • (2007) Mol Syst Biol. , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 95
    • 67649205713 scopus 로고    scopus 로고
    • A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide
    • Wren JD. A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. Bioinformatics. 2009;25:1694-701.
    • (2009) Bioinformatics. , vol.25 , pp. 1694-1701
    • Wren, J.D.1
  • 96
    • 77957338440 scopus 로고    scopus 로고
    • Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data
    • Zhou C, Yin Y, Dam P, Xu Y. Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data. J Proteome Res. 2010;9:5025-37.
    • (2010) J Proteome Res. , vol.9 , pp. 5025-5037
    • Zhou, C.1    Yin, Y.2    Dam, P.3    Xu, Y.4
  • 97
    • 79956010263 scopus 로고    scopus 로고
    • Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network
    • Liao Q, Liu C, Yuan X, Kang S, Miao R, Xiao H, et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res. 2011;39:3864-78.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 3864-3878
    • Liao, Q.1    Liu, C.2    Yuan, X.3    Kang, S.4    Miao, R.5    Xiao, H.6
  • 98
    • 77649168721 scopus 로고    scopus 로고
    • A general co-expression network-based approach to gene expression analysis: comparison and applications
    • Ruan J, Dean AK, Zhang W. A general co-expression network-based approach to gene expression analysis: comparison and applications. BMC Systems Biol. 2010;4:8.
    • (2010) BMC Systems Biol. , vol.4 , pp. 8
    • Ruan, J.1    Dean, A.K.2    Zhang, W.3
  • 99
    • 84875417100 scopus 로고    scopus 로고
    • Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks
    • Guo X, Gao L, Liao Q, Xiao H, Ma X, Yang X, et al. Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. Nucleic Acids Res. 2013;41:e35.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e35
    • Guo, X.1    Gao, L.2    Liao, Q.3    Xiao, H.4    Ma, X.5    Yang, X.6
  • 100
    • 84896722835 scopus 로고    scopus 로고
    • Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules
    • Xiao X, Moreno-Moral A, Rotival M, Bottolo L, Petretto E. Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules. PLoS Genet. 2014;10:e1004006.
    • (2014) PLoS Genet. , vol.10 , pp. e1004006
    • Xiao, X.1    Moreno-Moral, A.2    Rotival, M.3    Bottolo, L.4    Petretto, E.5
  • 101
    • 3042514191 scopus 로고    scopus 로고
    • Coexpression analysis of human genes across many microarray data sets
    • Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res. 2004;14:1085-94.
    • (2004) Genome Res. , vol.14 , pp. 1085-1094
    • Lee, H.K.1    Hsu, A.K.2    Sajdak, J.3    Qin, J.4    Pavlidis, P.5
  • 103
    • 84907485104 scopus 로고    scopus 로고
    • Vitamin D receptor-mediated stromal reprogramming suppresses pancreatitis and enhances pancreatic cancer therapy
    • Sherman MH, Yu RT, Engle DD, Ding N, Atkins AR, Tiriac H, et al. Vitamin D receptor-mediated stromal reprogramming suppresses pancreatitis and enhances pancreatic cancer therapy. Cell. 2014;159:80-93.
    • (2014) Cell. , vol.159 , pp. 80-93
    • Sherman, M.H.1    Yu, R.T.2    Engle, D.D.3    Ding, N.4    Atkins, A.R.5    Tiriac, H.6
  • 104
    • 77952367798 scopus 로고    scopus 로고
    • Widespread transcription at neuronal activity-regulated enhancers
    • Kim T-K, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465:182-7.
    • (2010) Nature. , vol.465 , pp. 182-187
    • Kim, T.-K.1    Hemberg, M.2    Gray, J.M.3    Costa, A.M.4    Bear, D.M.5    Wu, J.6
  • 105
    • 79961022267 scopus 로고    scopus 로고
    • Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters
    • Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol. 2011;18:956-63.
    • (2011) Nat Struct Mol Biol. , vol.18 , pp. 956-963
    • Koch, F.1    Fenouil, R.2    Gut, M.3    Cauchy, P.4    Albert, T.K.5    Zacarias-Cabeza, J.6
  • 107
    • 84937203002 scopus 로고    scopus 로고
    • Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency
    • Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, et al. Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency. Cell. 2015;162:412-24.
    • (2015) Cell. , vol.162 , pp. 412-424
    • Cacchiarelli, D.1    Trapnell, C.2    Ziller, M.J.3    Soumillon, M.4    Cesana, M.5    Karnik, R.6
  • 109
    • 0022919184 scopus 로고
    • Transfection of a DNA locus that mediates the conversion of 10T1/2 fibroblasts to myoblasts
    • Lassar AB, Paterson BM, Weintraub H. Transfection of a DNA locus that mediates the conversion of 10T1/2 fibroblasts to myoblasts. Cell. 1986;47:649-56.
    • (1986) Cell. , vol.47 , pp. 649-656
    • Lassar, A.B.1    Paterson, B.M.2    Weintraub, H.3
  • 110
    • 0029066359 scopus 로고
    • GATA-1 reprograms avian myelomonocytic cell lines into eosinophils, thromboblasts, and erythroblasts
    • Kulessa H, Frampton J, Graf T. GATA-1 reprograms avian myelomonocytic cell lines into eosinophils, thromboblasts, and erythroblasts. Genes Dev. 1995;9:1250-62.
    • (1995) Genes Dev. , vol.9 , pp. 1250-1262
    • Kulessa, H.1    Frampton, J.2    Graf, T.3
  • 112
    • 33747195353 scopus 로고    scopus 로고
    • Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
    • Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126:663-76.
    • (2006) Cell. , vol.126 , pp. 663-676
    • Takahashi, K.1    Yamanaka, S.2
  • 114
    • 53349178722 scopus 로고    scopus 로고
    • In vivo reprogramming of adult pancreatic exocrine cells to beta-cells
    • Zhou Q, Brown J, Kanarek A, Rajagopal J, Melton DA. In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature. 2008;455:627-32.
    • (2008) Nature. , vol.455 , pp. 627-632
    • Zhou, Q.1    Brown, J.2    Kanarek, A.3    Rajagopal, J.4    Melton, D.A.5
  • 115
    • 0019952768 scopus 로고
    • Fat-storing cells of the rat liver. Their isolation and purification
    • Knook D, Seffelaar A, de Leeuw AM. Fat-storing cells of the rat liver. Their isolation and purification. Exp Cell Res. 1982;139:468-71.
    • (1982) Exp Cell Res , vol.139 , pp. 468-471
    • Knook, D.1    Seffelaar, A.2    Leeuw, A.M.3


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