메뉴 건너뛰기




Volumn 11, Issue 1, 2016, Pages

A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; TRANSCRIPTOME;

EID: 84958787053     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0147514     Document Type: Article
Times cited : (34)

References (75)
  • 1
    • 33747278350 scopus 로고    scopus 로고
    • Considerations for non-invasive in-flight monitoring of astronaut immune status with potential use of MEMS and NEMS devices
    • WOS:000240216700001
    • Aponte VM, Finch DS, Klaus DM. Considerations for non-invasive in-flight monitoring of astronaut immune status with potential use of MEMS and NEMS devices. Life Sciences. 2006; 79(14):1317-33. doi: 10.1016/j.lfs.2006.04.007 PMID: WOS:000240216700001.
    • (2006) Life Sciences. , vol.79 , Issue.14 , pp. 1317-1333
    • Aponte, V.M.1    Finch, D.S.2    Klaus, D.M.3
  • 4
    • 0034622844 scopus 로고    scopus 로고
    • Mechanical culture conditions effect gene expression: Gravity-induced changes on the space shuttle
    • WOS:000089172700006
    • Hammond TG, Benes E, O'Reilly KC, Wolf DA, Linnehan RM, Taher A, et al. Mechanical culture conditions effect gene expression: gravity-induced changes on the space shuttle. Physiological Genomics. 2000; 3(3):163-73. PMID: WOS:000089172700006.
    • (2000) Physiological Genomics. , vol.3 , Issue.3 , pp. 163-173
    • Hammond, T.G.1    Benes, E.2    O'Reilly, K.C.3    Wolf, D.A.4    Linnehan, R.M.5    Taher, A.6
  • 5
    • 23044494757 scopus 로고    scopus 로고
    • Changes in gravitational force affect gene expression in developing organ systems at different developmental times
    • WOS:000234277900001
    • Shimada N, Sokunbi G, Moorman SJ. Changes in gravitational force affect gene expression in developing organ systems at different developmental times. Bmc Developmental Biology. 2005; 5. doi: 10. 1186/1471-213x-5-10 PMID: WOS:000234277900001.
    • (2005) Bmc Developmental Biology. , vol.5
    • Shimada, N.1    Sokunbi, G.2    Moorman, S.J.3
  • 6
    • 0036840426 scopus 로고    scopus 로고
    • Low-shear modeled microgravity alters the Salmonella enterica serovar typhimurium stress response in an RpoS-independent manner
    • WOS:000179027600026
    • Wilson JW, Ott CM, Ramamurthy R, Porwollik S, McClelland M, Pierson DL, et al. Low-shear modeled microgravity alters the Salmonella enterica serovar typhimurium stress response in an RpoS-independent manner. Applied and Environmental Microbiology. 2002; 68(11):5408-16. doi: 10.1128/aem.68. 11.5408-5416.2002 PMID: WOS:000179027600026.
    • (2002) Applied and Environmental Microbiology. , vol.68 , Issue.11 , pp. 5408-5416
    • Wilson, J.W.1    Ott, C.M.2    Ramamurthy, R.3    Porwollik, S.4    McClelland, M.5    Pierson, D.L.6
  • 10
    • 0141432227 scopus 로고    scopus 로고
    • Effects of the space flight environment on the immune system
    • MEDLINE:12875508
    • Sonnenfeld G, Butel JS, Shearer WT. Effects of the space flight environment on the immune system. Reviews on environmental health. 2003; 18(1):1-17. PMID: MEDLINE:12875508.
    • (2003) Reviews on Environmental Health. , vol.18 , Issue.1 , pp. 1-17
    • Sonnenfeld, G.1    Butel, J.S.2    Shearer, W.T.3
  • 11
    • 84894102367 scopus 로고    scopus 로고
    • Simulated microgravity increases heavy ion radiation-induced apoptosis in human B lymphoblasts
    • WOS:000331920800005
    • Dang B, Yang Y, Zhang E, Li W, Mi X, Meng Y, et al. Simulated microgravity increases heavy ion radiation-induced apoptosis in human B lymphoblasts. Life Sciences. 2014; 97(2):123-8. doi: 10.1016/j.lfs. 2013.12.008 PMID: WOS:000331920800005.
    • (2014) Life Sciences. , vol.97 , Issue.2 , pp. 123-128
    • Dang, B.1    Yang, Y.2    Zhang, E.3    Li, W.4    Mi, X.5    Meng, Y.6
  • 12
    • 23044511655 scopus 로고    scopus 로고
    • Exposure of human lymphocytes and lymphoblastoid cells to simulated microgravity strongly affects energy metabolism and DNA repair
    • WOS:000226763100003
    • Degan P, Sancandi M, Zunino A, Ottaggio L, Viaggi S, Cesarone F, et al. Exposure of human lymphocytes and lymphoblastoid cells to simulated microgravity strongly affects energy metabolism and DNA repair. Journal of Cellular Biochemistry. 2005; 94(3):460-9. doi: 10.1002/jcb.20302 PMID: WOS:000226763100003.
    • (2005) Journal of Cellular Biochemistry. , vol.94 , Issue.3 , pp. 460-469
    • Degan, P.1    Sancandi, M.2    Zunino, A.3    Ottaggio, L.4    Viaggi, S.5    Cesarone, F.6
  • 13
    • 84920704004 scopus 로고    scopus 로고
    • Lymphoblastoid Cell lines: A Continuous in Vitro Source of Cells to Study Carcinogen Sensitivity and DNA Repair
    • MEDLINE:24551762
    • Hussain T, Mulherkar R. Lymphoblastoid Cell lines: a Continuous in Vitro Source of Cells to Study Carcinogen Sensitivity and DNA Repair. International journal of molecular and cellular medicine. 2012; 1 (2):75-87. PMID: MEDLINE:24551762.
    • (2012) International Journal of Molecular and Cellular Medicine. , vol.1 , Issue.2 , pp. 75-87
    • Hussain, T.1    Mulherkar, R.2
  • 14
    • 80053144962 scopus 로고    scopus 로고
    • A decade of exploring the cancer epigenome - Biological and translational implications
    • WOS:000295155600012
    • Baylin SB, Jones PA. A decade of exploring the cancer epigenome - biological and translational implications. Nature Reviews Cancer. 2011; 11(10):726-34. doi: 10.1038/nrc3130 PMID: WOS:000295155600012.
    • (2011) Nature Reviews Cancer. , vol.11 , Issue.10 , pp. 726-734
    • Baylin, S.B.1    Jones, P.A.2
  • 15
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genome-wide DNA methylation analysis
    • 20125086
    • Laird PW. Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet. 2010; 11(3):191-203. doi: 10.1038/nrg2732 PMID: 20125086
    • (2010) Nat Rev Genet. , vol.11 , Issue.3 , pp. 191-203
    • Laird, P.W.1
  • 16
    • 84856058152 scopus 로고    scopus 로고
    • Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers
    • MEDLINE:21896958
    • Haffner MC, Chaux A, Meeker AK, Esopi DM, Gerber J, Pellakuru LG, et al. Global 5-hydroxymethylcytosine content is significantly reduced in tissue stem/progenitor cell compartments and in human cancers. Oncotarget. 2011; 2(8):627-37. PMID: MEDLINE:21896958.
    • (2011) Oncotarget. , vol.2 , Issue.8 , pp. 627-637
    • Haffner, M.C.1    Chaux, A.2    Meeker, A.K.3    Esopi, D.M.4    Gerber, J.5    Pellakuru, L.G.6
  • 17
    • 84864129535 scopus 로고    scopus 로고
    • Distribution of 5-hydroxymethylcytosine in different human tissues
    • MEDLINE:21772996
    • Li W, Liu M. Distribution of 5-hydroxymethylcytosine in different human tissues. Journal of nucleic acids. 2011; 2011:870726. PMID: MEDLINE:21772996. doi: 10.4061/2011/870726
    • (2011) Journal of Nucleic Acids. , vol.2011 , pp. 870726
    • Li, W.1    Liu, M.2
  • 18
    • 79960064353 scopus 로고    scopus 로고
    • Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation
    • MEDLINE:21723200
    • Moran-Crusio K, Reavie L, Shih A, Abdel-Wahab O, Ndiaye-Lobry D, Lobry C, et al. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell. 2011; 20 (1):11-24. PMID: MEDLINE:21723200. doi: 10.1016/j.ccr.2011.06.001
    • (2011) Cancer Cell. , vol.20 , Issue.1 , pp. 11-24
    • Moran-Crusio, K.1    Reavie, L.2    Shih, A.3    Abdel-Wahab, O.4    Ndiaye-Lobry, D.5    Lobry, C.6
  • 19
    • 84897489039 scopus 로고    scopus 로고
    • The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts
    • 24555846
    • Wagner JR. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biology. 2014; 15(2):R37. doi: 10.1186/gb-2014-15-2-r37 PMID: 24555846
    • (2014) Genome Biology. , vol.15 , Issue.2 , pp. R37
    • Wagner, J.R.1
  • 20
    • 84929628130 scopus 로고    scopus 로고
    • Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation
    • 25074712
    • Lou S. Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biology. 2014; 15(7):408. doi: 10.1186/s13059-014-0408-0 PMID: 25074712
    • (2014) Genome Biology. , vol.15 , Issue.7 , pp. 408
    • Lou, S.1
  • 21
    • 84868198427 scopus 로고    scopus 로고
    • Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia
    • 23064414
    • Kulis M. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nature Genetics. 2012; 44(11):1236-43. doi: 10.1038/ng.2443 PMID: 23064414
    • (2012) Nature Genetics. , vol.44 , Issue.11 , pp. 1236-1243
    • Kulis, M.1
  • 22
    • 77954504873 scopus 로고    scopus 로고
    • Conserved role of intragenic DNA methylation in regulating alternative promoters
    • 20613842
    • Maunakea AK. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010; 466(7303):253-8. doi: 10.1038/nature09165 PMID: 20613842
    • (2010) Nature , vol.466 , Issue.7303 , pp. 253-258
    • Maunakea, A.K.1
  • 23
    • 84924309893 scopus 로고    scopus 로고
    • Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation
    • Jun W. Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation. BMC Genomics. 2015; 16(1):1-12. doi: 10.1186/s12864-015-1271-4
    • (2015) BMC Genomics. , vol.16 , Issue.1 , pp. 1-12
    • Jun, W.1
  • 24
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores
    • 19151715
    • Rafael AI, Christine L-A, Bo W, Zhijin W, Carolina M, Patrick O, et al. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nature Genetics. 2009; 41(2):178. doi: 10.1038/ng.298 PMID: 19151715
    • (2009) Nature Genetics. , vol.41 , Issue.2 , pp. 178
    • Rafael, A.I.1    Christine, L.-A.2    Bo, W.3    Zhijin, W.4    Carolina, M.5    Patrick, O.6
  • 25
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • 22641018
    • Peter AJ. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature Reviews Genetics. 2012; 13(7):484. doi: 10.1038/nrg3230 PMID: 22641018
    • (2012) Nature Reviews Genetics. , vol.13 , Issue.7 , pp. 484
    • Peter, A.J.1
  • 26
    • 66149146320 scopus 로고    scopus 로고
    • Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
    • WOS:000266048800037
    • Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1. Science. 2009; 324 (5929):930-5. doi: 10.1126/science.1170116 PMID: WOS:000266048800037.
    • (2009) Science , vol.324 , Issue.5929 , pp. 930-935
    • Tahiliani, M.1    Koh, K.P.2    Shen, Y.3    Pastor, W.A.4    Bandukwala, H.5    Brudno, Y.6
  • 27
    • 66149123748 scopus 로고    scopus 로고
    • The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain
    • WOS:000266048800036
    • Kriaucionis S, Heintz N. The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain. Science. 2009; 324(5929):929-30. doi: 10.1126/science.1169786 PMID: WOS:000266048800036.
    • (2009) Science , vol.324 , Issue.5929 , pp. 929-930
    • Kriaucionis, S.1    Heintz, N.2
  • 28
    • 84864722177 scopus 로고    scopus 로고
    • 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription
    • WOS:000307153600016
    • Kellinger MW, Song CX, Chong J, Lu XY, He C, Wang D. 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription. Nature Structural & Molecular Biology. 2012; 19(8):831-3. doi: 10.1038/nsmb.2346 PMID: WOS:000307153600016.
    • (2012) Nature Structural & Molecular Biology. , vol.19 , Issue.8 , pp. 831-833
    • Kellinger, M.W.1    Song, C.X.2    Chong, J.3    Lu, X.Y.4    He, C.5    Wang, D.6
  • 29
    • 60449090499 scopus 로고    scopus 로고
    • Spaceflight induces both transient and heritable alterations in DNA methylation and gene expression in rice (Oryza sativa L.)
    • WOS:000264580800009
    • Ou X, Long L, Zhang Y, Xue Y, Liu J, Lin X, et al. Spaceflight induces both transient and heritable alterations in DNA methylation and gene expression in rice (Oryza sativa L.). Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis. 2009; 662(1-2):44-53. doi: 10.1016/j.mrfmmm. 2008.12.004 PMID: WOS:000264580800009.
    • (2009) Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis , vol.662 , Issue.1-2 , pp. 44-53
    • Ou, X.1    Long, L.2    Zhang, Y.3    Xue, Y.4    Liu, J.5    Lin, X.6
  • 30
    • 77957143992 scopus 로고    scopus 로고
    • Simulated microgravity-induced epigenetic changes in human lymphocytes
    • WOS:000281690500015
    • Singh KP, Kumari R, DuMond JW. Simulated Microgravity-Induced Epigenetic Changes in Human Lymphocytes. Journal of Cellular Biochemistry. 2010; 111(1):123-9. doi: 10.1002/jcb.22674 PMID: WOS:000281690500015.
    • (2010) Journal of Cellular Biochemistry , vol.111 , Issue.1 , pp. 123-129
    • Singh, K.P.1    Kumari, R.2    DuMond, J.W.3
  • 31
    • 78049497364 scopus 로고    scopus 로고
    • Spaceflight-induced genetic and epigenetic changes in the rice (Oryza sativa L.) genome are independent of each other
    • 20616874
    • Ou X, Long L, Wu Y, Yu Y, Lin X, Qi X, et al. Spaceflight-induced genetic and epigenetic changes in the rice (Oryza sativa L.) genome are independent of each other. Genome. 2010; 53(7):524-32. doi: 10. 1139/g10-030 PMID: 20616874.
    • (2010) Genome. , vol.53 , Issue.7 , pp. 524-532
    • Ou, X.1    Long, L.2    Wu, Y.3    Yu, Y.4    Lin, X.5    Qi, X.6
  • 32
    • 0028829796 scopus 로고
    • Establishment and characterization of a novel cell-line, TK-6, derived from T-cell blast crisis of chronic myelogenous leukemia, with the secretion of parathyroid hormonerelated protein
    • WOS:A1995TG56200021
    • Watanabe T, Kataoka T, Mizuta S, Kobayashi M, Uchida T, Imai K, et al. ESTABLISHMENT AND CHARACTERIZATION OF A NOVEL CELL-LINE, TK-6, DERIVED FROM T-CELL BLAST CRISIS OF CHRONIC MYELOGENOUS LEUKEMIA, WITH THE SECRETION OF PARATHYROID HORMONERELATED PROTEIN. Leukemia. 1995; 9(11):1926-34. PMID: WOS:A1995TG56200021.
    • (1995) Leukemia. , vol.9 , Issue.11 , pp. 1926-1934
    • Watanabe, T.1    Kataoka, T.2    Mizuta, S.3    Kobayashi, M.4    Uchida, T.5    Imai, K.6
  • 33
    • 84872716339 scopus 로고    scopus 로고
    • Ground-based facilities for simulation of microgravity: Organism-specific recommendations for their use, and recommended terminology
    • 23252378
    • Herranz R. Ground-based facilities for simulation of microgravity: organism-specific recommendations for their use, and recommended terminology. Astrobiology. 2013; 13(1):1. doi: 10.1089/ast.2012.0876 PMID: 23252378
    • (2013) Astrobiology. , vol.13 , Issue.1 , pp. 1
    • Herranz, R.1
  • 34
    • 80052783075 scopus 로고    scopus 로고
    • Effects of simulated microgravity on expression profile of MicroRNA in human lymphoblastoid cells
    • WOS:000294726800058
    • Mangala LS, Zhang Y, He Z, Emami K, Ramesh GT, Story M, et al. Effects of Simulated Microgravity on Expression Profile of MicroRNA in Human Lymphoblastoid Cells. Journal of Biological Chemistry. 2011; 286(37):32483-90. doi: 10.1074/jbc.M111.267765 PMID: WOS:000294726800058.
    • (2011) Journal of Biological Chemistry , vol.286 , Issue.37 , pp. 32483-32490
    • Mangala, L.S.1    Zhang, Y.2    He, Z.3    Emami, K.4    Ramesh, G.T.5    Story, M.6
  • 35
    • 77957344240 scopus 로고    scopus 로고
    • AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay
    • WOS:000284183700005
    • Butcher LM, Beck S. AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay. Methods. 2010; 52(3):223-31. doi: 10.1016/j.ymeth.2010.04.003 PMID: WOS:000284183700005.
    • (2010) Methods. , vol.52 , Issue.3 , pp. 223-231
    • Butcher, L.M.1    Beck, S.2
  • 37
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • 19451168 PubMed Central PMCID: PMC2705234. Epub 2009/05/20
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. Epub 2009/05/20. doi: 10.1093/bioinformatics/btp324 PMID: 19451168; PubMed Central PMCID: PMC2705234.
    • (2009) Bioinformatics. , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 38
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • 19505943
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
    • (2009) Bioinformatics. , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6
  • 39
    • 84876344321 scopus 로고    scopus 로고
    • Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers
    • 23587164
    • Wilson G, Dhami P, Feber A, Cortazar D, Suzuki Y, Schulz R, et al. Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers. GigaScience. 2012; 1(1):3. doi: 10.1186/2047-217X-1-3 PMID: 23587164
    • (2012) GigaScience. , vol.1 , Issue.1 , pp. 3
    • Wilson, G.1    Dhami, P.2    Feber, A.3    Cortazar, D.4    Suzuki, Y.5    Schulz, R.6
  • 41
    • 60849117520 scopus 로고    scopus 로고
    • Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks
    • 19061503 PubMed Central PMCID: PMC2628906. Epub 2008/12/09
    • Nix DA, Courdy SJ, Boucher KM. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC bioinformatics. 2008; 9:523. Epub 2008/12/09. doi: 10.1186/1471-2105-9-523 PMID: 19061503; PubMed Central PMCID: PMC2628906.
    • (2008) BMC Bioinformatics. , vol.9 , pp. 523
    • Nix, D.A.1    Courdy, S.J.2    Boucher, K.M.3
  • 42
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • WOS:000261591300019
    • Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nature Biotechnology. 2008; 26(12):1351-9. doi: 10.1038/nbt.1508 PMID: WOS:000261591300019.
    • (2008) Nature Biotechnology. , vol.26 , Issue.12 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 43
    • 79955564639 scopus 로고    scopus 로고
    • Measuring reproducibility of high-throughput experiments
    • WOS:000300382500003
    • Li Q, Brown JB, Huang H, Bickel PJ. MEASURING REPRODUCIBILITY OF HIGH-THROUGHPUT EXPERIMENTS. Annals of Applied Statistics. 2011; 5(3):1752-79. doi: 10.1214/11-aoas466 PMID: WOS:000300382500003.
    • (2011) Annals of Applied Statistics , vol.5 , Issue.3 , pp. 1752-1779
    • Li, Q.1    Brown, J.B.2    Huang, H.3    Bickel, P.J.4
  • 44
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • WOS:000275243500019
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. doi: 10.1093/bioinformatics/btq033 PMID: WOS:000275243500019.
    • (2010) Bioinformatics. , vol.26 , Issue.6 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 45
    • 33747836850 scopus 로고    scopus 로고
    • CEAS: Cis-regulatory element annotation system
    • WOS:000245650200110
    • Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Research. 2006; 34:W551-W4. doi: 10.1093/nar/gkl322 PMID: WOS:000245650200110.
    • (2006) Nucleic Acids Research. , vol.34 , pp. W551-W554
    • Ji, X.1    Li, W.2    Song, J.3    Wei, L.4    Liu, X.S.5
  • 46
    • 77955183656 scopus 로고    scopus 로고
    • PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci
    • WOS:000281443000002
    • Salmon-Divon M, Dvinge H, Tammoja K, Bertone P. PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci. Bmc Bioinformatics. 2010; 11. doi: 10.1186/1471-2105-11-415 PMID: WOS:000281443000002.
    • (2010) Bmc Bioinformatics. , vol.11
    • Salmon-Divon, M.1    Dvinge, H.2    Tammoja, K.3    Bertone, P.4
  • 47
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • 19289445 PubMed Central PMCID: PMC2672628. Epub 2009/03/18
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105-11. Epub 2009/03/18. doi: 10.1093/bioinformatics/btp120 PMID: 19289445; PubMed Central PMCID: PMC2672628.
    • (2009) Bioinformatics. , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 48
    • 84874312025 scopus 로고    scopus 로고
    • NGSUtils: A software suite for analyzing and manipulating next-generation sequencing datasets
    • 23314324 PubMed Central PMCID: PMC3570212. Epub 2013/01/15
    • Breese MR, Liu Y. NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. Bioinformatics. 2013; 29(4):494-6. Epub 2013/01/15. doi: 10.1093/bioinformatics/bts731 PMID: 23314324; PubMed Central PMCID: PMC3570212.
    • (2013) Bioinformatics. , vol.29 , Issue.4 , pp. 494-496
    • Breese, M.R.1    Liu, Y.2
  • 49
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • 19505943 PubMed Central PMCID: PMC2723002. Epub 2009/06/10
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. Epub 2009/06/10. doi: 10.1093/bioinformatics/btp352 PMID: 19505943; PubMed Central PMCID: PMC2723002.
    • (2009) Bioinformatics. , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6
  • 50
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • 19910308 PubMed Central PMCID: PMC2796818. Epub 2009/11/17
    • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26(1):139-40. Epub 2009/11/17. doi: 10. 1093/bioinformatics/btp616 PMID: 19910308; PubMed Central PMCID: PMC2796818.
    • (2010) Bioinformatics. , vol.26 , Issue.1 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 51
    • 84864494098 scopus 로고    scopus 로고
    • GeneCodis3: A non-redundant and modular enrichment analysis tool for functional genomics
    • 22573175 (Web Server issue)
    • Tabas-Madrid D. GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. Nucleic Acids Research. 2012; 40(Web Server issue):W478. doi: 10.1093/nar/gks402 PMID: 22573175
    • (2012) Nucleic Acids Research. , vol.40 , pp. W478
    • Tabas-Madrid, D.1
  • 52
    • 84865777819 scopus 로고    scopus 로고
    • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    • 22955991
    • Landt SG. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 2012; 22(9):1813. doi: 10.1101/gr.136184.111 PMID: 22955991
    • (2012) Genome Research. , vol.22 , Issue.9 , pp. 1813
    • Landt, S.G.1
  • 53
    • 84894573097 scopus 로고    scopus 로고
    • Large-scale quality analysis of published ChIP-seq data
    • WOS:000331614800002
    • Marinov GK, Kundaje A, Park PJ, Wold BJ. Large-Scale Quality Analysis of Published ChIP-seq Data. G3-Genes Genomes Genetics. 2014; 4(2):209-23. doi: 10.1534/g3.113.008680 PMID: WOS:000331614800002
    • (2014) G3-Genes Genomes Genetics , vol.4 , Issue.2 , pp. 209-223
    • Marinov, G.K.1    Kundaje, A.2    Park, P.J.3    Wold, B.J.4
  • 54
    • 77952214662 scopus 로고    scopus 로고
    • GREAT improves functional interpretation of cis-regulatory regions
    • WOS:000277452700030
    • McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnology. 2010; 28(5):495-U155. doi: 10.1038/nbt. 1630 PMID: WOS:000277452700030.
    • (2010) Nature Biotechnology. , vol.28 , Issue.5 , pp. 495-555
    • McLean, C.Y.1    Bristor, D.2    Hiller, M.3    Clarke, S.L.4    Schaar, B.T.5    Lowe, C.B.6
  • 55
    • 79952535972 scopus 로고    scopus 로고
    • Regulation and function of DNA methylation in plants and animals
    • WOS:000288064900007
    • He X-J, Chen T, Zhu J-K. Regulation and function of DNA methylation in plants and animals. Cell Research. 2011; 21(3):442-65. doi: 10.1038/cr.2011.23 PMID: WOS:000288064900007.
    • (2011) Cell Research. , vol.21 , Issue.3 , pp. 442-465
    • He, X.-J.1    Chen, T.2    Zhu, J.-K.3
  • 57
    • 0032190057 scopus 로고    scopus 로고
    • P53 is involved in but not required for ionizing radiation-induced caspase-3 activation and apoptosis in human lymphoblast cell lines
    • WOS:000076219100015
    • Yu YJ, Little JB. p53 is involved in but not required for ionizing radiation-induced caspase-3 activation and apoptosis in human lymphoblast cell lines. Cancer Research. 1998; 58(19):4277-81. PMID: WOS:000076219100015.
    • (1998) Cancer Research. , vol.58 , Issue.19 , pp. 4277-4281
    • Yu, Y.J.1    Little, J.B.2
  • 58
    • 33749037187 scopus 로고    scopus 로고
    • Chromosomal instability correlates with genome-wide DNA demethylation in human primary colorectal cancers
    • 16951157
    • Rodriguez J, Frigola J, Vendrell E, Risques R-A, Fraga M, Morales C, et al. Chromosomal Instability Correlates with Genome-wide DNA Demethylation in Human Primary Colorectal Cancers. Cancer Research. 2006; 66(17):8462-9468. PMID: 16951157
    • (2006) Cancer Research , vol.66 , Issue.17 , pp. 8462-9468
    • Rodriguez, J.1    Frigola, J.2    Vendrell, E.3    Risques, R.-A.4    Fraga, M.5    Morales, C.6
  • 59
    • 10044297379 scopus 로고    scopus 로고
    • Baseline levels of chromosome instability in the human lymphoblastoid cell TK6
    • WOS:000225258300008
    • Schwartz JL, Jordan R, Evans HH, Lenarczyk M, Liber HL. Baseline levels of chromosome instability in the human lymphoblastoid cell TK6. Mutagenesis. 2004; 19(6):477-82. doi: 10.1093/mutage/geh060 PMID: WOS:000225258300008.
    • (2004) Mutagenesis. , vol.19 , Issue.6 , pp. 477-482
    • Schwartz, J.L.1    Jordan, R.2    Evans, H.H.3    Lenarczyk, M.4    Liber, H.L.5
  • 60
    • 0014333021 scopus 로고
    • Human lymphoblastoid lines from lymph node and spleen
    • WOS:A1968B745800004
    • Levy JA, Virolain M, Defendi V. HUMAN LYMPHOBLASTOID LINES FROM LYMPH NODE AND SPLEEN. Cancer. 1968; 22(3):517-&. doi: 10.1002/1097-0142(196809)22:3<517::aidcncr2820220305>3.0.co;2-a PMID: WOS:A1968B745800004.
    • (1968) Cancer , vol.22 , Issue.3 , pp. 517
    • Levy, J.A.1    Virolain, M.2    Defendi, V.3
  • 61
    • 80053357385 scopus 로고    scopus 로고
    • Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor
    • WOS:000296299500002
    • Londin ER, Keller MA, D'Andrea MR, Delgrosso K, Ertel A, Surrey S, et al. Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor. Bmc Genomics. 2011; 12. doi: 10.1186/1471-2164-12-464 PMID: WOS:000296299500002.
    • (2011) Bmc Genomics. , vol.12
    • Londin, E.R.1    Keller, M.A.2    D'Andrea, M.R.3    Delgrosso, K.4    Ertel, A.5    Surrey, S.6
  • 62
    • 84958800466 scopus 로고    scopus 로고
    • Identification of putative major space genes using genome-wide literature data
    • style = "font-size:10.5pt s, line-height:115%, font-family:"Georgia" s, mso-fareast-font-family:Calibri, mso-bidi-font-family:, WBL Roman" TN, et al. editor
    • style = "font-size:10.5pt s, line-height:115%, font-family:"Georgia" s, mso-fareast-font-family:Calibri, mso-bidi-font-family:, Roman" TN, et al. Identification of Putative Major Space Genes Using Genome-Wide Literature Data. In: Hammond Timothy G. WBL, Birdsall Holly H. and Clement Jade Q., editor. Biotechnology: InTech; 2015.
    • (2015) Biotechnology: InTech
    • Hammond Timothy, G.1    Birdsall Holly, H.2    Clement Jade, Q.3
  • 63
    • 11244351579 scopus 로고    scopus 로고
    • Function and regulation of Cullin-RING ubiquitin ligases
    • WOS:000226109300010
    • Petroski MD, Deshaies RJ. Function and regulation of Cullin-RING ubiquitin ligases. Nature Reviews Molecular Cell Biology. 2005; 6(1):9-20. doi: 10.1038/nrm1547 PMID: WOS:000226109300010.
    • (2005) Nature Reviews Molecular Cell Biology. , vol.6 , Issue.1 , pp. 9-20
    • Petroski, M.D.1    Deshaies, R.J.2
  • 64
    • 34248354813 scopus 로고    scopus 로고
    • The yeast ubiquitin ligase SCFMet30: Connecting environmental and intracellular conditions to cell division
    • WOS:000207723600016
    • Kaiser P, Su N-Y, Yen JL, Ouni I, Flick K. The yeast ubiquitin ligase SCFMet30: connecting environmental and intracellular conditions to cell division. Cell Division. 2006; 1. doi: 10.1186/1747-1028-1-16 PMID: WOS:000207723600016.
    • (2006) Cell Division. , vol.1
    • Kaiser, P.1    Su, N.-Y.2    Yen, J.L.3    Ouni, I.4    Flick, K.5
  • 65
    • 84868088696 scopus 로고    scopus 로고
    • Signal-induced disassembly of the SCF ubiquitin ligase complex by Cdc48/p97
    • WOS:000310423800014
    • Yen JL, Flick K, Papagiannis CV, Mathur R, Tyrrell A, Ouni I, et al. Signal-Induced Disassembly of the SCF Ubiquitin Ligase Complex by Cdc48/p97. Molecular Cell. 2012; 48(2):288-97. doi: 10.1016/j. molcel.2012.08.015 PMID: WOS:000310423800014.
    • (2012) Molecular Cell. , vol.48 , Issue.2 , pp. 288-297
    • Yen, J.L.1    Flick, K.2    Papagiannis, C.V.3    Mathur, R.4    Tyrrell, A.5    Ouni, I.6
  • 66
    • 33751232939 scopus 로고    scopus 로고
    • Regulation of the cadmium stress response through SCF-like ubiquitin ligases: Comparison between Saccharomyces cerevisiae, Schizosaccharomyces pombe and mammalian cells
    • WOS:000242961300015
    • Baudouin-Cornu P, Labarre J. Regulation of the cadmium stress response through SCF-like ubiquitin ligases: comparison between Saccharomyces cerevisiae, Schizosaccharomyces pombe and mammalian cells. Biochimie. 2006; 88(11):1673-85. doi: 10.1016/j.biochi.2006.03.001 PMID: WOS:000242961300015.
    • (2006) Biochimie. , vol.88 , Issue.11 , pp. 1673-1685
    • Baudouin-Cornu, P.1    Labarre, J.2
  • 67
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • 17334365
    • Michael W, Ines H, Michael BS, Liliana R, Svante P, Michael R, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genetics. 2007; 39(4):457. doi: 10.1038/ng1990 PMID: 17334365
    • (2007) Nature Genetics. , vol.39 , Issue.4 , pp. 457
    • Michael, W.1    Ines, H.2    Michael, B.S.3    Liliana, R.4    Svante, P.5    Michael, R.6
  • 68
    • 79960688508 scopus 로고    scopus 로고
    • DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
    • 21251332
    • Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biology. 2011; 12 (1):R10-R. doi: 10.1186/gb-2011-12-1-r10 PMID: 21251332
    • (2011) Genome Biology. , vol.12 , Issue.1 , pp. R10-R
    • Bell, J.T.1    Pai, A.A.2    Pickrell, J.K.3    Gaffney, D.J.4    Pique-Regi, R.5    Degner, J.F.6
  • 69
    • 79952265169 scopus 로고    scopus 로고
    • A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues (Gene Regulation by DNA Methylation in Primates)
    • 21383968
    • Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y. A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues (Gene Regulation by DNA Methylation in Primates). PLoS Genetics. 2011; 7(2):e1001316. doi: 10.1371/journal.pgen.1001316 PMID: 21383968
    • (2011) PLoS Genetics. , vol.7 , Issue.2
    • Pai, A.A.1    Bell, J.T.2    Marioni, J.C.3    Pritchard, J.K.4    Gilad, Y.5
  • 70
    • 84928723198 scopus 로고    scopus 로고
    • The hypomethylating agent Decitabine causes a paradoxical increase in 5-hydroxymethylcytosine in human leukemia cells
    • WOS:000353281700001
    • Chowdhury B, McGovern A, Cui Y, Choudhury SR, Cho I-H, Cooper B, et al. The hypomethylating agent Decitabine causes a paradoxical increase in 5-hydroxymethylcytosine in human leukemia cells. Scientific Reports. 2015; 5. doi: 10.1038/srep09281 PMID: WOS:000353281700001.
    • (2015) Scientific Reports. , vol.5
    • Chowdhury, B.1    McGovern, A.2    Cui, Y.3    Choudhury, S.R.4    Cho, I.-H.5    Cooper, B.6
  • 71
    • 64349091471 scopus 로고    scopus 로고
    • Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells
    • 19329998
    • Madeleine PB, Jin Billy L, Yuan G, Je-Hyuk L, Emily ML, In-Hyun P, et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature Biotechnology. 2009; 27 (4):361. doi: 10.1038/nbt.1533 PMID: 19329998
    • (2009) Nature Biotechnology. , vol.27 , Issue.4 , pp. 361
    • Madeleine, P.B.1    Jin Billy, L.2    Yuan, G.3    Je-Hyuk, L.4    Emily, M.L.5    In-Hyun, P.6
  • 73
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • WOS:000271899300037
    • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009; 462(7271):315-22. doi: 10. 1038/nature08514 PMID: WOS:000271899300037.
    • (2009) Nature , vol.462 , Issue.7271 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3    Hawkins, R.D.4    Hon, G.5    Tonti-Filippini, J.6
  • 74
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • 19829295
    • Ryan L, Mattia P, Robert HD, Hawkins RD, Gary H, Julian T-F, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009; 462(7271):315. doi: 10.1038/nature08514 PMID: 19829295
    • (2009) Nature , vol.462 , Issue.7271 , pp. 315
    • Ryan, L.1    Mattia, P.2    Robert, H.D.3    Hawkins, R.D.4    Gary, H.5    Julian, T.-F.6
  • 75
    • 7544231794 scopus 로고    scopus 로고
    • Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells
    • Matthew CL, David RD, Mike S, Mark G. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nature Structural & Molecular Biology. 2004; 11(11):1068. doi: 10.1038/nsmb840
    • (2004) Nature Structural & Molecular Biology. , vol.11 , Issue.11 , pp. 1068
    • Matthew, C.L.1    David, R.D.2    Mike, S.3    Mark, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.