Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
Open accessAbstract
Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex–next-generation sequencing (M-NGS). Hidden Markov model–based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ∼12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively ( P -value < 2 × 10 −16 ). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.
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Statistically significant correlations observed between DNA methylation and gene expression accounted for relatively small effects.
“The statistically significant correlations that were observed, however, accounted for relatively small effects.”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [138]
Pairwise DNA-methylation and RNA-seq integration has mostly consisted of the analysis of the correlation between DEGs and methylation patterns.
“Pairwise DNA-methylation and RNA-seq integration, for the most part, has consisted of the analysis of the correlation between DEGs and methylation patterns [138–140].”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [138]
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Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., & Speleman, F. (2002) · Genome Biology · doi:10.1186/gb-2002-3-7-research0034 · Cited by 20,038 · see citing works
In silico prediction of protein-protein interactions in human macrophages
Souiai, O., Guerfali, F. Z., Miled, S. B., Brun, C., & Benkahla, A. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-157 · Cited by 10,785 · see citing works
Significance analysis of microarrays applied to the ionizing radiation response
Tusher, V. G., Tibshirani, R., & Chu, G. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.091062498 · Cited by 10,568 · see citing works
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124 · see citing works
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361 · see citing works
Jones, P. A., & Baylin, S. B. (2007) · Cell · doi:10.1016/j.cell.2007.01.029 · Cited by 4,515 · see citing works
MethPrimer: designing primers for methylation PCRs
Li, L.-C., & Dahiya, R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.11.1427 · Cited by 2,741 · see citing works
Genome-scale DNA methylation maps of pluripotent and differentiated cells
Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536 · see citing works
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Cokus, S. J., Feng, S.-H., Zhang, X.-Y., Chen, Z., Merriman, B., Haudenschild, C., Pradhan, S., Nelson, S., Pellegrini, M., & Jacobsen, S. (2008) · Nature · doi:10.1038/nature06745 · Cited by 2,278 · see citing works
Irizarry, R. A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M., et al. (2009) · Nature Genetics · doi:10.1038/ng.298 · Cited by 2,177 · see citing works
Rhodes, D. R., Sundaram, S. K., Mahavisno, V., Varambally, R., Yu, J., Briggs, B., Barrette, T. R., Anstett, M. J., Kincead-Beal, C., Kulkarni, P., et al. (2007) · Neoplasia · doi:10.1593/neo.07112 · Cited by 2,064 · see citing works
Self-citationA Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R., & Young, R. A. (2007) · Cell · doi:10.1016/j.cell.2007.05.042 · Cited by 1,946 · see citing works
Weber, M., Davies, J. J., Wittig, D., Oakeley, E., Haase, M., Lam, W., & Schübeler, D. (2005) · Nature Genetics · doi:10.1038/ng1598 · Cited by 1,885 · see citing works
Conserved role of intragenic DNA methylation in regulating alternative promoters
Maunakea, A. K., Nagarajan, R. P., Bilenky, M., Ballinger, T. J., D’Souza, C., Fouse, S. D., Johnson, B. E., Hong, C., Nielsen, C., Zhao, Y., et al. (2010) · Nature · doi:10.1038/nature09165 · Cited by 1,743 · see citing works
Principles and challenges of genome-wide DNA methylation analysis
Laird, P. W. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2732 · Cited by 1,574 · see citing works
Comprehensive analysis of CpG islands in human chromosomes 21 and 22
Takai, D., & Jones, P. A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.052410099 · Cited by 1,507 · see citing works
DNA methylation profiling of human chromosomes 6, 20 and 22
Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V. K., Attwood, J., Burger, M., Burton, J. H., Cox, T. V., Davies, R., Down, T. A., et al. (2006) · Nature Genetics · doi:10.1038/ng1909 · Cited by 1,350 · see citing works
The genomic complexity of primary human prostate cancer
Berger, M. F., Lawrence, M. S., Demichelis, F., Drier, Y., Cibulskis, K., Sivachenko, A., Sboner, A., Esgueva, R., Pflueger, D., Sougnez, C. L., et al. (2011) · Nature · doi:10.1038/nature09744 · Cited by 1,213 · see citing works
CpG island methylator phenotype in cancer
Issa, J. J. (2004) · Nature reviews. Cancer · doi:10.1038/nrc1507 · Cited by 1,107 · see citing works
Dammann, R., Li, C., Yoon, J., Chin, P. L., Bates, S., & Pfeifer, G. P. (2000) · Nature Genetics · doi:10.1038/77083 · Cited by 1,064 · see citing works
Integrative molecular concept modeling of prostate cancer progression
Tomlins, S. A., Mehra, R., Rhodes, D. R., Cao, X., Wang, L., Dhanasekaran, S. M., Sundaram, S. K., Wei, J. T., Rubin, M. A., Pienta, K. J., et al. (2006) · Nature Genetics · doi:10.1038/ng1935 · Cited by 909 · see citing works
Self-citationDistinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer
Tomlins, S., Laxman, B., Dhanasekaran, S., Helgeson, B. E., Cao, X.-H., Morris, D. S., Menon, A., Jing, X.-J., Cao, Q., Han, B., et al. (2007) · Nature · doi:10.1038/nature06024 · Cited by 904 · see citing works
Self-citationTranscriptome sequencing to detect gene fusions in cancer
Maher, C. A., Kumar‐Sinha, C., Cao, X., Sundaram, S. K., Han, B., Jing, X., Sam, L. T., Barrette, T. R., Palanisamy, N., & Chinnaiyan, A. M. (2009) · Nature · doi:10.1038/nature07638 · Cited by 887 · see citing works
Self-citationIllingworth, R. S., & Bird, A. P. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.04.012 · Cited by 881 · see citing works
Yu, J., Yu, J., Mani, R.-S., Cao, Q., Brenner, C. J., Cao, X., Wang, X., Wu, L., Li, J., Hu, M., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.03.018 · Cited by 850 · see citing works
Self-citationHarris, R. A., Wang, T., Coarfa, C., Nagarajan, R. P., Hong, C., Downey, S. L., Johnson, B., Fouse, S. D., Delaney, A. D., Zhao, Y., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1682 · Cited by 713 · see citing works
Recurrent gene fusions in prostate cancer
Kumar‐Sinha, C., Tomlins, S. A., & Chinnaiyan, A. M. (2008) · Nature reviews. Cancer · doi:10.1038/nrc2402 · Cited by 663 · see citing works
Self-citationA Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Down, T. A., Rakyan, V. K., Turner, D., Flicek, P., Li, H., Kulesha, E., Gräf, S., Johnson, N., Herrero, J., Tomazou, E. M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1414 · Cited by 651 · see citing works
A census of mammalian imprinting
Morison, I. M., Ramsay, J. P., & Spencer, H. G. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.06.008 · Cited by 645 · see citing works
CpG islands influence chromatin structure via the CpG-binding protein Cfp1
Thomson, J. P., Skene, P. J., Selfridge, J., Clouaire, T., Guy, J., Webb, S., Kerr, A. R. W., Deaton, A., Andrews, R., James, K. D., et al. (2010) · Nature · doi:10.1038/nature08924 · Cited by 625 · see citing works
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J., & Lengauer, T. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti652 · Cited by 617 · see citing works
Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes
Wu, H., Coskun, V., Tao, J., Xie, W., Ge, W., Yoshikawa, K., Li, E., Zhang, Y., & Sun, Y. E. (2010) · Science · doi:10.1126/science.1190485 · Cited by 604 · see citing works
Quantitative comparison of genome-wide DNA methylation mapping technologies
Bock, C., Tomazou, E. M., Brinkman, A. B., Müller, F., Simmer, F., Gu, H., Jäger, N., Gnirke, A., Stunnenberg, H. G., & Meissner, A. (2010) · Nature Biotechnology · doi:10.1038/nbt.1681 · Cited by 587 · see citing works
Hypermethylation of CpG Islands in Primary and Metastatic Human Prostate Cancer
Yegnasubramanian, S., Kowalski, J., Gonzalgo, M. L., ZAHURAK, M. L., Piantadosi, S., Walsh, P. C., Bova, G. S., Marzo, A. M. D., Isaacs, W. B., & Nelson, W. G. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-3972 · Cited by 527 · see citing works
Schummer, M., Ng, W. V., Bumgarner, R. E., Nelson, P. S., Schummer, B., Bednarski, D. W., Hassell, L., Baldwin, R. L., Karlan, B. Y., & Hood, L. (1999) · Gene · doi:10.1016/s0378-1119(99)00342-x · Cited by 402 · see citing works
A human B cell methylome at 100−base pair resolution
Rauch, T. A., Wu, X., Zhong, X., Riggs, A. D., & Pfeifer, G. P. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812399106 · Cited by 333 · see citing works
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
Gu, H., Bock, C., Mikkelsen, T. S., Jäger, N., Smith, Z. D., Tomazou, E. M., Gnirke, A., Lander, E. S., & Meissner, A. (2010) · Nature Methods · doi:10.1038/nmeth.1414 · Cited by 324 · see citing works
Epigenetic Changes in Prostate Cancer: Implication for Diagnosis and Treatment
Li, L., Carroll, P. R., & Dahiya, R. (2005) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/dji010 · Cited by 299 · see citing works
Yegnasubramanian, S., Haffner, M. C., Zhang, Y., Gürel, B., Cornish, T. C., Wu, Z. J., Irizarry, R. A., Morgan, J., Hicks, J. L., DeWeese, T. L., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-6088 · Cited by 297 · see citing works
Brunner, A. L., Johnson, D. S., Kim, S. W., Valouev, A., Reddy, T. E., Neff, N. F., Anton, E., Medina, C., Nguyen, L., Chiao, E. T., et al. (2009) · Genome Research · doi:10.1101/gr.088773.108 · Cited by 283 · see citing works
Reuter, M., Chuma, S., Tanaka, T. S. T., Franz, T., Stark, A., & Pillai, R. S. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1615 · Cited by 256 · see citing works
Ashida, S., Nakagawa, H., Katagiri, T., Furihata, M., Iiizumi, M., Anazawa, Y., Tsunoda, T., Takata, R., Kasahara, K., Miki, T., et al. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-0020 · Cited by 239 · see citing works
Hodges, E. C., Smith, A. D., Kendall, J., Xuan, Z., Ravi, K., Rooks, M. G., Zhang, M. Q., Ye, K. Q., Bhattacharjee, A., Brizuela, L., et al. (2009) · Genome Research · doi:10.1101/gr.095190.109 · Cited by 236 · see citing works
Proteins with whey-acidic-protein motifs and cancer
Bouchard, D., Morisset, D., Bourbonnais, Y., & Tremblay, G. M. (2006) · The Lancet Oncology · doi:10.1016/s1470-2045(06)70579-4 · Cited by 204 · see citing works
The tumor suppressor RASSF1A in human carcinogenesis: an update.
Dammann, R., Schagdarsurengin, U., Seidel, C., Strunnikova, M., Rastetter, M., Baier, K., & Pfeifer, G. P. (2005) · PubMed · doi:10.14670/hh-20.645 · Cited by 197 · see citing works
PubMeth: a cancer methylation database combining text-mining and expert annotation
Ongenaert, M., Neste, L. V., Meyer, T. D., Menschaert, G., Bekaert, S., & Criekinge, W. V. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm788 · Cited by 175 · see citing works
Kuzmin, I., Gillespie, J. W., Protopopov, A. I., Geil, L., Dreijerink, K. M. A., Yang, Y., Vocke, C. D., Duh, F.-M. C., Zabarovsky, E. R., Minna, J. D., et al. (2002) · PubMed · Cited by 158 · see citing works
Han, B., Mehra, R., Dhanasekaran, S. M., Yu, J., Menon, A., Lonigro, R. J., Wang, X., Gong, Y., Wang, L., Shankar, S., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-08-2014 · Cited by 154 · see citing works
Self-citationMinireview: Epigenetic Alterations in Human Prostate Cancers
Nelson, W. G., Marzo, A. M. D., & Yegnasubramanian, S. (2009) · Endocrinology · doi:10.1210/en.2009-0573 · Cited by 143 · see citing works
Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs
Rhodes, D. R., Sundaram, S. K., Tomlins, S. A., Mahavisno, V., Kasper, N. M., Varambally, R., Barrette, T. R., Ghosh, D., Varambally, S., & Chinnaiyan, A. M. (2007) · Neoplasia · doi:10.1593/neo.07292 · Cited by 142 · see citing works
Self-citationThe epigenome as a therapeutic target in prostate cancer
Perry, A. S., Watson, R. W. G., Lawler, M., & Hollywood, D. P. (2010) · Nature Reviews Urology · doi:10.1038/nrurol.2010.185 · Cited by 134 · see citing works
Gebhard, C., Benner, C. W., Ehrich, M., Schwarzfischer, L., Schilling, E., Klug, M., Dietmaier, W., Thiede, C., Holler, E., Andreesen, R., et al. (2010) · Cancer Research · doi:10.1158/0008-5472.can-09-3406 · Cited by 123 · see citing works
Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression
Kim, J. H., Dhanasekaran, S. M., Mehra, R., Tomlins, S. A., Gu, W., Yu, J., Kumar‐Sinha, C., Cao, X., Dash, A., Wang, L., et al. (2007) · Cancer Research · doi:10.1158/0008-5472.can-07-1297 · Cited by 122 · see citing works
Self-citationComparative methylome analysis of benign and malignant peripheral nerve sheath tumorsPreprint
Feber, A., Wilson, G. A., Zhang, L., Presneau, N., Idowu, B. D., Down, T. A., Rakyan, V. K., Noon, L. A., Lloyd, A. C., Stupka, E., et al. (2011) · Genome Research · doi:10.1101/gr.109678.110 · Cited by 115 · see citing works
HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
Qin, Z. S., Yu, J., Shen, J., Maher, C. A., Hu, M., Sundaram, S. K., Yu, J., & Chinnaiyan, A. M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-369 · Cited by 102 · see citing works
Self-citationDiscovery of Novel Hypermethylated Genes in Prostate Cancer Using Genomic CpG Island Microarrays
Kron, K. J., Pethe, V. V., Briollais, L., Sadiković, B., Özçelik, H., Sunderji, A., Venkateswaran, V., Pinthus, J. H., Fleshner, N. E., van der Kwast, T., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004830 · Cited by 91 · see citing works
The MIRA Method for DNA Methylation Analysis
Rauch, T. A., & Pfeifer, G. P. (2008) · Methods in molecular biology · doi:10.1007/978-1-59745-522-0_6 · Cited by 72 · see citing works
Reduced Expression of IRF7 in Nasal Epithelial Cells from Smokers after Infection with Influenza
Jaspers, I., Horvath, K. M., Zhang, W., Brighton, L. E., Carson, J. L., & Noah, T. L. (2009) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2009-0254oc · Cited by 63 · see citing works
Jhavar, S. G., Reid, A. H. M., Clark, J., Kote‐Jarai, Z., Christmas, T. J., Thompson, A. C., Woodhouse, C. R. J., Ogden, C. W., Fisher, C., CORBISHLEY, C. M., et al. (2007) · Journal of Molecular Diagnostics · doi:10.2353/jmoldx.2008.070085 · Cited by 58 · see citing works
Global Reactivation of Epigenetically Silenced Genes in Prostate Cancer
Ibragimova, I., de Cáceres, I. I., Hoffman, A. M., Potapova, A., Dulaimi, E., Al‐Saleem, T., Hudes, G. R., Ochs, M. F., & Cairns, P. (2010) · Cancer Prevention Research · doi:10.1158/1940-6207.capr-10-0039 · Cited by 49 · see citing works
Flagged first, then by citations
1 of the 61 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
The Molecular Taxonomy of Primary Prostate Cancer
Abeshouse, A. A., Ahn, J., Akbani, R., Ally, A., Amin, S. B., Andry, C., Annala, M., Aprikian, A. G., Armenia, J., Arora, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.10.025 · Cited by 3,082 · see citing works
A survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794 · see citing works
Targeting epigenetic modifications in cancer therapy: erasing the roadmap to cancer
Mohammad, H. P., Barbash, O., & Creasy, C. L. (2019) · Nature Medicine · doi:10.1038/s41591-019-0376-8 · Cited by 418 · see citing works
The DNA methylation landscape of advanced prostate cancer
Zhao, S. G., Chen, W. S., Li, H., Foye, A., Zhang, M., Sjöström, M., Aggarwal, R. R., Playdle, D., Liao, A., Alumkal, J. J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0648-8 · Cited by 351 · see citing works
Self-citationTumor origin detection with tissue-specific miRNA and DNA methylation markers
Tang, W., Wan, S., Yang, Z., Teschendorff, A. E., & Zou, Q. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx622 · Cited by 347 · see citing works
iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition
Liu, Z., Xiao, X., Qiu, W., & Chou, K. (2015) · Analytical Biochemistry · doi:10.1016/j.ab.2014.12.009 · Cited by 252 · see citing works
Global Methylation Patterns in Idiopathic Pulmonary Fibrosis
Rabinovich, E. I., Kapetanaki, M. G., Steinfeld, I., Gibson, K. F., Pandit, K. V., Yu, G., Zohar Yakhini, B., & Kaminski, N. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033770 · Cited by 197 · see citing works
Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies
Du, W., & Elemento, O. (2014) · Oncogene · doi:10.1038/onc.2014.291 · Cited by 182 · see citing works
Sox2 Is an Androgen Receptor-Repressed Gene That Promotes Castration-Resistant Prostate Cancer
Kregel, S., Kiriluk, K. J., Rosen, A. M., Cai, Y., Reyes, E. E., Otto, K. B., Tom, W. R., Paner, G. P., Szmulewitz, R. Z., & Griend, D. J. V. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053701 · Cited by 174 · see citing works
The importance of DNA methylation in prostate cancer development
Massie, C. E., Mills, I. G., & Lynch, A. G. (2016) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/j.jsbmb.2016.04.009 · Cited by 158 · see citing works
ICGC Project on Early Onset Prostate Cancer, Gu, L., Frommel, S. C., Oakes, C. C., Simon, R., Grupp, K., Gerig, C. Y., Bär, D., Robinson, M. D., Baer, C. R., et al. (2014) · Nature Genetics · doi:10.1038/ng.3165 · Cited by 150 · see citing works
Random forest-based modelling to detect biomarkers for prostate cancer progression
Tóth, R., Schiffmann, H., Hube‐Magg, C., Büscheck, F., Höflmayer, D., Weidemann, S. A., Lebok, P., Fraune, C., Minner, S. J. P., Schlomm, T., et al. (2019) · Clinical Epigenetics · doi:10.1186/s13148-019-0736-8 · Cited by 141 · see citing works
Rauluševičiūtė, I., Drabløs, F., & Rye, M. B. (2020) · BMC Medical Genomics · doi:10.1186/s12920-020-0657-6 · Cited by 129 · see citing works
Börno, S. T., Fischer, A., Kerick, M., Fälth, M., Laible, M., Brase, J. C., Kuner, R., Dahl, A., Grimm, C., Sayanjali, B., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0041 · Cited by 133 · see citing works
Virtues and Weaknesses of DNA Methylation as a Test for Cervical Cancer Prevention
Lorincz, A. T. (2016) · Acta Cytologica · doi:10.1159/000450595 · Cited by 126 · see citing works
Molecular pathways and targets in prostate cancer
Shtivelman, E., Beer, T. M., & Evans, C. P. (2014) · Oncotarget · doi:10.18632/oncotarget.2406 · Cited by 115 · see citing works
Molecular Subtypes of Prostate Cancer
Arora, K., & Barbieri, C. E. (2018) · Current Oncology Reports · doi:10.1007/s11912-018-0707-9 · Cited by 116 · see citing works
Clinical advances in targeting epigenetics for cancer therapy
Feng, S., & Carvalho, D. D. D. (2021) · FEBS Journal · doi:10.1111/febs.15750 · Cited by 107 · see citing works
Prognostic DNA Methylation Markers for Prostate Cancer
Strand, S. H., Orntoft, T. F., & Sørensen, K. D. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms150916544 · Cited by 101 · see citing works
Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer
Ma, J., Gnanasekar, A., Lee, A., Li, W. T., Haas, M., Wang‐Rodriguez, J., Chang, E. Y., Rajasekaran, M. R., & Ongkeko, W. M. (2020) · Cancers · doi:10.3390/cancers12092524 · Cited by 100 · see citing works
Effects of phthalate exposure on asthma may be mediated through alterations in DNA methylation
Wang, I.-J., Karmaus, W. J., Chen, S.-L., Holloway, J. W., & Ewart, S. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0060-x · Cited by 97 · see citing works
Alkhateeb, A., Rezaeian, I., Singireddy, S., Cavallo‐Medved, D., Porter, L. A., & Rueda, L. G. (2019) · Cancer Informatics · doi:10.1177/1176935119835522 · Cited by 86 · see citing works
Perinatal bisphenol A exposure promotes dose-dependent alterations of the mouse methylome
Kim, J. H., Sartor, M. A., Rozek, L. S., Faulk, C. D., Anderson, O. S., Jones, T. R., Nahar, M. S., & Dolinoy, D. C. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-30 · Cited by 82 · see citing works
Self-citationGenome-wide CpG island methylation analyses in non-small cell lung cancer patients
Heller, G., Babinsky, V. N., Ziegler, B., Weinzierl, M., Noll, C., Altenberger, C., Müllauer, L., Dekan, G., Grin, Y., Láng, G., et al. (2012) · Carcinogenesis · doi:10.1093/carcin/bgs363 · Cited by 82 · see citing works
Schoenborn, J. R., Nelson, P., & Fang, M. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-3606 · Cited by 80 · see citing works
Chen, J., Zhang, D., Yan, W., Yang, D., & Shen, B. (2013) · BioMed Research International · doi:10.1155/2013/901578 · Cited by 78 · see citing works
Epigenomic Alterations in Localized and Advanced Prostate Cancer
Lin, P., Γιαννοπούλου, Ε., Park, K., Mosquera, J. M., Sboner, A., Tewari, A. K., Garraway, L. A., Beltran, H., Rubin, M. A., & Elemento, O. (2013) · Neoplasia · doi:10.1593/neo.122146 · Cited by 78 · see citing works
DNA methylation status is more reliable than gene expression at detecting cancer in prostate biopsy
Paziewska, A., Dąbrowska, M., Goryca, K., Antoniewicz, A. A., Dobruch, J. T., Mikuła, M., Jarosz, D., Zapała, Ł., Borówka, A., & Ostrowski, J. (2014) · British Journal of Cancer · doi:10.1038/bjc.2014.337 · Cited by 76 · see citing works
Global DNA hypomethylation in prostate cancer development and progression: a systematic review
Zelić, R., Fiano, V., Grasso, C., Zugna, D., Pettersson, A., Gillio‐Tos, A., Merletti, F., & Richiardi, L. (2014) · Prostate Cancer and Prostatic Diseases · doi:10.1038/pcan.2014.45 · Cited by 74 · see citing works
Self-citationPhytochemicals in cancer prevention: modulating epigenetic alterations of DNA methylation
Pop, S., Enciu, A., Ţârcomnicu, I., Gille, E., & Tănase, C. (2019) · Phytochemistry Reviews · doi:10.1007/s11101-019-09627-x · Cited by 73 · see citing works
Targeting Histone Methylation in Cancer
McCabe, M. T., Mohammad, H. P., Barbash, O., & Kruger, R. G. (2017) · The Cancer Journal · doi:10.1097/ppo.0000000000000283 · Cited by 73 · see citing works
Wang, Z., Li, X., Jiang, Y. W., Shao, Q., Liu, Q., Chen, B., & Huang, D. (2015) · PLoS ONE · doi:10.1371/journal.pone.0132866 · Cited by 70 · see citing works
Cancer diagnostic classifiers based on quantitative DNA methylation
Lorincz, A. T. (2014) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2014.897610 · Cited by 70 · see citing works
Saied, M. H., Marzec, J., Khalid, S., Smith, P., Down, T. A., Rakyan, V. K., Molloy, G., Raghavan, M., Debernardi, S., & Young, B. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033213 · Cited by 67 · see citing works
DNA Methylation as Clinically Useful Biomarkers—Light at the End of the Tunnel
Levenson, V., & Melnikov, A. A. (2012) · Pharmaceuticals · doi:10.3390/ph5010094 · Cited by 66 · see citing works
DNA methylation of microRNA genes in multiple myeloma
Wong, K. Y., Huang, X., & Chim, C. S. (2012) · Carcinogenesis · doi:10.1093/carcin/bgs212 · Cited by 65 · see citing works
dos Reis, M. B., Barros‐Filho, M. C., Marchi, F. A., Beltrami, C. M., Kuasne, H., Pinto, C. A. L., Ambatipudi, S., Herceg, Z., Kowalski, L. P., & Rogatto, S. R. (2017) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2017-00881 · Cited by 65 · see citing works
Kim, J. W., Kim, S., Turner, A. R., Young, T., Smith, S. G., Liu, W., Lindberg, J., Egevad, L., Grönberg, H., Isaacs, W. B., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048455 · Cited by 64 · see citing works
Self-citationLi, Y., Zhang, Y., Li, S., Lu, J., Chen, J., Wang, Y., Li, Y., Xu, J., & Li, X. (2015) · Scientific Reports · doi:10.1038/srep08790 · Cited by 63 · see citing works
Faulk, C. D., Kim, J. H., Jones, T. R., McEachin, R. C., Nahar, M. S., Dolinoy, D. C., & Sartor, M. A. (2015) · Current Zoology · doi:10.1093/eep/dvv006 · Cited by 62 · see citing works
Self-citationRhee, J., Kim, K., Chae, H., Evans, J. M., Yan, P. S., Zhang, B.-T., Gray, J. W., Spellman, P. T., Huang, T. H. ‐., Nephew, K. P., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt643 · Cited by 61 · see citing works
Theodore, S., Davis, M. B., Zhao, F., Wang, H., Chen, D., Rhim, J. S., Dean-Colomb, W. M., Turner, T., Ji, W., Zeng, G., et al. (2014) · Oncotarget · doi:10.18632/oncotarget.1953 · Cited by 60 · see citing works
DNA Methylation Changes in Prostate Cancer
Goering, W., Kloth, M. T., & Schulz, W. A. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-612-8_4 · Cited by 60 · see citing works
Kron, K. J., Liu, L., Trudel, D., Pethe, V. V., Trachtenberg, J., Fleshner, N. E., Bapat, B. V., & van der Kwast, T. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-11-2901 · Cited by 59 · see citing works
Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue
Geybels, M. S., Zhao, S., Wong, C.-J., Bibikova, M. V., Klotzle, B., Wu, M. C., Ostrander, E. A., Fan, J., Feng, Z., & Stanford, J. L. (2015) · The Prostate · doi:10.1002/pros.23093 · Cited by 58 · see citing works
Yu, Y. P., Ding, Y., Chen, R., Liao, S. G., Ren, B., Michalopoulos, A., Michalopoulos, G. K., Nelson, J. B., Tseng, G. C., & Luo, J. (2013) · American Journal Of Pathology · doi:10.1016/j.ajpath.2013.08.018 · Cited by 57 · see citing works
Faulk, C. D., Kim, J. H., Anderson, O. S., Nahar, M. S., Jones, T. R., Sartor, M. A., & Dolinoy, D. C. (2016) · Epigenetics · doi:10.1080/15592294.2016.1183856 · Cited by 55 · see citing works
Self-citationKirby, M. K., Ramaker, R. C., Roberts, B. S., Lasseigne, B. N., Gunther, D. S., Burwell, T. C., Davis, N. S., Gulzar, Z. G., Absher, D., Cooper, S. J., et al. (2017) · BMC Cancer · doi:10.1186/s12885-017-3252-2 · Cited by 55 · see citing works
Parrillo, L., Costa, V., Raciti, G. A., Longo, M., Spinelli, R., Esposito, R., Nigro, C., Vastolo, V., Desiderio, A., Zatterale, F., et al. (2016) · International Journal of Obesity · doi:10.1038/ijo.2016.36 · Cited by 52 · see citing works
Luo, J., Ding, Y., Chen, R., Michalopoulos, G. K., Nelson, J. B., Tseng, G. C., & Yu, Y. P. (2013) · American Journal Of Pathology · doi:10.1016/j.ajpath.2013.02.040 · Cited by 50 · see citing works
Prostate cancer epigenetic biomarkers: next-generation technologies
Valdés‐Mora, F., & Clark, S. J. (2014) · Oncogene · doi:10.1038/onc.2014.111 · Cited by 49 · see citing works
Lipid Metabolism and Epigenetics Crosstalk in Prostate Cancer
Pardo, J. C. T., de Porras, V. R., Gil, J., Pous, A. F., Puig‐Domingo, M., & Jordà, M. (2022) · Nutrients · doi:10.3390/nu14040851 · Cited by 50 · see citing works
Esposito, S., Russo, M. V., Airoldi, I., Tupone, M. G., Sorrentino, C., Barbarito, G., Meo, S. D., & Carlo, E. D. (2015) · Oncotarget · doi:10.18632/oncotarget.2736 · Cited by 49 · see citing works
Bhasin, J., Lee, B., Matkin, L., Taylor, M. G., Hu, B., Xu, Y., Magi‐Galluzzi, C., Klein, E. A., & Ting, A. H. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.10.078 · Cited by 48 · see citing works
Hájková, H., Marková, J., Haškovec, C., Šárová, I., Fuchs, O., Kostečka, A., Cetkovský, P., Michalova, K., & Schwarz, J. (2012) · Leukemia Research · doi:10.1016/j.leukres.2012.05.012 · Cited by 47 · see citing works
Wyatt, A. W., Mo, F., Wang, Y. Z., & Collins, C. C. (2013) · Asian Journal of Andrology · doi:10.1038/aja.2013.13 · Cited by 46 · see citing works
Møller, M., Strand, S. H., Mundbjerg, K., Liang, G., Gill, I. S., Haldrup, C., Borre, M., Høyer, S., Orntoft, T. F., & Sørensen, K. D. (2017) · Scientific Reports · doi:10.1038/srep40636 · Cited by 45 · see citing works
Li, Y., Camarillo, C., Xu, J., Arana, T. B., Xiao, Y., Zhao, Z., Chen, H., Ramírez, M., Zavala, J., Escamilla, M., et al. (2015) · BioMed Research International · doi:10.1155/2015/201587 · Cited by 42 · see citing works
Using Epigenome-Wide Association Scans of DNA Methylation in Age-Related Complex Human Traits
Tsai, P.-C., Spector, T. D., & Bell, J. T. (2012) · Epigenomics · doi:10.2217/epi.12.45 · Cited by 41 · see citing works
Heterogeneous epigenetic regulation ofTIMP3in prostate cancer
Shinojima, T., Yu, Q., Huang, S. K., Li, M., Mizuno, R., Liu, E. T., Hoon, D. S. �., & Lessard, L. (2012) · Epigenetics · doi:10.4161/epi.22333 · Cited by 41 · see citing works
Geybels, M. S., Alumkal, J. J., Luedeke, M., Rinckleb, A. E., Zhao, S., Shui, I. M., Bibikova, M. V., Klotzle, B., van den Brandt, P. A., Ostrander, E. A., et al. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0161-6 · Cited by 41 · see citing works
Kukkonen, K., Taavitsainen, S., Huhtala, L., Uusi-Mäkelä, J., Granberg, K. J., Nykter, M., & Urbanucci, A. (2021) · Cancers · doi:10.3390/cancers13133325 · Cited by 41 · see citing works
Hartung, T., Zhang, L., Kanwar, R., Khrebtukova, I., Reinhardt, M., Wang, C., Therneau, T. M., Banck, M. S., Schroth, G. P., & Beutler, A. S. (2012) · Epigenetics · doi:10.4161/epi.19565 · Cited by 35 · see citing works
SFRP1 repression in prostate cancer is triggered by two different epigenetic mechanisms
García-Tobilla, P., Solórzano, S. R., Salido-Guadarrama, I., González-Covarrubias, V., Morales-Montor, G., Díaz‐Otañez, C. E., & Rodríguez‐Dorantes, M. (2016) · Gene · doi:10.1016/j.gene.2016.08.030 · Cited by 36 · see citing works
Han, J., Liu, S., Sun, Z., Zhang, Y., Zhang, F., Zhang, C., Shang, D., Yang, H., Su, F., Xu, Y., et al. (2017) · Scientific Reports · doi:10.1038/srep46566 · Cited by 36 · see citing works
Human methionine synthase A2756G polymorphism increases susceptibility to prostate cancer
Shao, H., Ren, K., Gao, S., Zou, J.-G., Mi, Y., Zhang, L.-F., Zuo, L., Okada, A., & Yasui, T. (2018) · Aging · doi:10.18632/aging.101509 · Cited by 36 · see citing works
Raheem, O. A., Kulidjian, A., Wu, C. N., Jeong, Y. B., Yamaguchi, T., Smith, K. M., Goff, D. J., Leu, H. S., Morris, S., Cacalano, N. A., et al. (2011) · Journal of Translational Medicine · doi:10.1186/1479-5876-9-185 · Cited by 36 · see citing works
Nüsgen, N., Goering, W., Daukša, A., Biswas, A., Jamil, M. A., Dimitriou, I. M., Sharma, A., Singer, H., Fimmers, R., Fröhlich, H., et al. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0051-y · Cited by 35 · see citing works
Jiang, Y., Liu, S., Chen, X. '., Cao, Y., & Tao, Y. (2012) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2012.12.003 · Cited by 35 · see citing works
Chen, D.-P., Lin, Y., & Fann, C. S. J. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw018 · Cited by 35 · see citing works
DNA Methylation-Guided Prediction of Clinical Failure in High-Risk Prostate Cancer
Litovkin, K., Eynde, A. V., Joniau, S., Lerut, E., Laenen, A., Gevaert, T., Gevaert, O., Spahn, M., Kneitz, B., Gramme, P., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130651 · Cited by 35 · see citing works
Varışlı, L. (2013) · Genetic Testing and Molecular Biomarkers · doi:10.1089/gtmb.2012.0524 · Cited by 35 · see citing works
Tian, F., Zhan, F., VanderKraats, N. D., Hiken, J., Edwards, J. R., Zhang, H., Zhao, K., & Song, J. (2013) · Epigenetics · doi:10.4161/epi.24361 · Cited by 35 · see citing works
Copy-number-aware differential analysis of quantitative DNA sequencing dataPreprint
Robinson, M. D., Strbenac, D., Stirzaker, C., Statham, A. L., Song, J. Z., Speed, T. P., & Clark, S. J. (2012) · Genome Research · doi:10.1101/gr.139055.112 · Cited by 35 · see citing works
Functional roles of antisense enhancer RNA for promoting prostate cancer progression
Pan, C., Wen, S., Chen, L., Wei, Y., Niu, Y., & Zhao, Y. (2020) · Theranostics · doi:10.7150/thno.51931 · Cited by 29 · see citing works
The evolution of CpG density and lifespan in conserved primate and mammalian promoters
McLain, A. T., & Faulk, C. D. (2018) · Aging · doi:10.18632/aging.101413 · Cited by 32 · see citing works
Pan, J., Chen, J., Zhang, B., Chen, X., Huang, B., Zhuang, J., Mo, C., & Qiu, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075283 · Cited by 31 · see citing works
DKK1 and Kremen Expression Predicts the Osteoblastic Response to Bone Metastasis
Clines, K. L., & Clines, G. A. (2018) · Translational Oncology · doi:10.1016/j.tranon.2018.04.013 · Cited by 31 · see citing works
Targeting the methionine addiction of cancer.
Sedillo, J. C., & Cryns, V. L. (2022) · PubMed Central · Cited by 30 · see citing works
Recent advances in understanding DNA methylation of prostate cancer
Shin, H. J., Hua, J. T., & Li, H. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1182727 · Cited by 32 · see citing works
Peng, Y., Song, Y., & Wang, H. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.723466 · Cited by 29 · see citing works
The Genomic Landscape of Prostate Cancer
Spans, L., Clinckemalie, L., Helsen, C., Vanderschueren, D., Boonen, S., Lerut, E., Joniau, S., & Claessens, F. (2013) · International Journal of Molecular Sciences · doi:10.3390/ijms140610822 · Cited by 29 · see citing works
Pan, J., Chen, Y., Mo, C., Wang, D., Chen, J., Mao, X., Guo, S., Zhuang, J., & Qiu, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092815 · Cited by 29 · see citing works
Patel, L. R., Nykter, M., Chen, K., & Zhang, W. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.10.018 · Cited by 28 · see citing works
Singh, R. K., Srivastava, A., Ponnusamy, K., Manvati, S., Chopra, R., & Bamezai, R. N. K. (2014) · Scientific Reports · doi:10.1038/srep06571 · Cited by 28 · see citing works
Kacprzyk, L. A., Laible, M., Andrasiuk, T., Brase, J. C., Börno, S. T., Fälth, M., Kuner, R., Lehrach, H. R., Schweiger, M. R., & Sültmann, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059976 · Cited by 28 · see citing works
Haldrup, C., Lynnerup, A.-S., Storebjerg, T. M., Vang, S., Wild, P. J., Visakorpi, T., Arsov, C., Schulz, W. A., Lindberg, J., Grönberg, H., et al. (2016) · Molecular Oncology · doi:10.1016/j.molonc.2016.02.001 · Cited by 28 · see citing works
Daniūnaitė, K., Bakavičius, A., Žukauskaitė, K., Rauluševičiūtė, I., Lazutka, J. R., Ulys, A., Jankevičius, F., & Jarmalaitė, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22116091 · Cited by 28 · see citing works
Zseq: An Approach for Preprocessing Next-Generation Sequencing Data
Alkhateeb, A., & Rueda, L. G. (2017) · Journal of Computational Biology · doi:10.1089/cmb.2017.0021 · Cited by 27 · see citing works
Investigative pathology: leading the post-genomic revolution
Berman, D. M., Bosenberg, M., Orwant, R., Thurberg, B. L., Draetta, G. F., Fletcher, C. D. �., & Loda, M. F. (2011) · Laboratory Investigation · doi:10.1038/labinvest.2011.147 · Cited by 27 · see citing works
Kron, K. J., Trudel, D., Pethe, V. V., Briollais, L., Fleshner, N. E., van der Kwast, T., & Bapat, B. V. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-3139 · Cited by 26 · see citing works
Erfani, S. F., Hua, H., Pan, Y.-Y., Zhou, B., & Yang, X.-W. H. (2021) · Cancers · doi:10.3390/cancers13092005 · Cited by 20 · see citing works
Kuroyanagi, J., Shimada, Y., Zhang, B., Ariyoshi, M., Umemoto, N., Nishimura, Y., & Tanaka, T. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.07.033 · Cited by 26 · see citing works
Danziger, O., Shai, B., Sabo, Y., Bacharach, E., & Ehrlich, M. (2016) · Oncotarget · doi:10.18632/oncotarget.10313 · Cited by 25 · see citing works
Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression
Li, Y., Vongsangnak, W., Chen, L., & Shen, B. (2014) · BMC Medical Genomics · doi:10.1186/1755-8794-7-s1-s3 · Cited by 24 · see citing works
Cruz, S. P., Zhang, Q., Devarajan, R., Paia, C., Luo, B., Zhang, K., Koivusalo, S., Qin, L., Xia, J., Ahtikoski, A. M., et al. (2024) · Advanced Science · doi:10.1002/advs.202305547 · Cited by 23 · see citing works
Common gene pathways and families altered by DNA methylation in breast and prostate cancers
Day, T. K., & Bianco‐Miotto, T. (2013) · Endocrine Related Cancer · doi:10.1530/erc-13-0204 · Cited by 23 · see citing works
Identification of specific DNA methylation sites on the Y-chromosome as biomarker in prostate cancer
Yao, L., Ren, S., Zhang, M., Du, F., Zhu, Y., Yu, H., Zhang, C., Li, X., Yang, C., Liu, H., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.6141 · Cited by 22 · see citing works
Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Li, J.-L., Mazar, J., Zhong, C., Faulkner, G. J., Govindarajan, S. S., Zhang, Z., Dinger, M. E., Meredith, G., Adams, C., Zhang, S., et al. (2013) · Scientific Reports · doi:10.1038/srep02962 · Cited by 21 · see citing works
Manipulating the epigenome for the treatment of urological malignancies
O’Rourke, C. J., Knabben, V., Bolton, E. M., Moran, D. C., Lynch, T. H., Hollywood, D. P., & Perry, A. S. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.007 · Cited by 21 · see citing works
- Authors
- Kim, J. H., Dhanasekaran, S. M., Prensner, J. R., Cao, X., Robinson, D., Kalyana-Sundaram, S., Huang, C., Shankar, S., Jing, X., Iyer, M., Hu, M., Sam, L., Grasso, C., Maher, C. A., Palanisamy, N., Mehra, R., Kominsky, H. D., Siddiqui, J., Yu, J., Qin, Z. S., & Chinnaiyan, A. M.
- Affiliations
- University of Michigan (US)
- Harvard University (US)
- Northwestern University (US)
- Emory University (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-07
- Volume
- 21
- Issue
- 7
- Pages
- 1028-1041
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3129246
- OpenAlex
- W2114884175
- Cited by
- 188
- References
- 61
- Citations by year
- 2026: 7 · 2025: 2 · 2024: 4 · 2023: 4 · 2022: 7 · 2021: 9 · 2020: 11 · 2019: 12 · 2018: 8 · 2017: 15 · 2016: 14 · 2015: 20 · 2014: 20 · 2013: 25 · 2012: 27
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- U.S. Department of Defense (W81XWH, BC075023)
- Howard Hughes Medical Institute
- Prostate Cancer Foundation
- Amgen
- University of Michigan (P50CA69568)
- Canary Foundation
- National Institutes of Health (W81XWH, CA009676)
- National Institute on Drug Abuse (U54DA021519)
- National Human Genome Research Institute (R01HG005119)
- National Cancer Institute (P50-CA-69568, R01CA132874, U01CA111275, CA009676-18, R00CA129565, K99CA129565, P50CA069568, T32CA009676)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Prostate Cancer Treatment and Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
- Keywords
- prostate cancer, DNA methylation, methylome, promoter methylation, CpG island methylation, differentially methylated regions, HE4, H3K4me3, tumor progression, metastatic prostate cancer, epigenetic regulation
- MeSH terms
- DNA, Neoplasm, Epithelial Cells, Humans, Male, Markov Chains, Neoplasm Metastasis, Promoter Regions, Genetic, Prostate, Prostatic Neoplasms, Gene Library, Polymerase Chain Reaction, Sequence Analysis, RNA, CpG Islands, DNA Methylation, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Transcription Initiation Site, Cell Line, Tumor, Epigenomics, High-Throughput Nucleotide Sequencing
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