Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Open accessAbstract
Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for example, TERC, which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2 and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles and by integrating these data with RNA-seq data obtained from melanoma cells, we have identified a co-expression network of differentially methylated genes with significance for cancer related functions. Focused assays of melanoma patient tissue samples for CpG island methylation near the noncoding RNA gene SNORD-10 demonstrated high specificity.
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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 [139]
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 [139]
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,477 · see citing works
Circos: An information aesthetic for comparative genomicsPreprint
Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,838 · see citing works
Network biology: understanding the cell's functional organization
Barabási, A.-L., & Oltvai, Z. N. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1272 · Cited by 7,903 · see citing works
Oncomirs — microRNAs with a role in cancer
Esquela‐Kerscher, A., & Slack, F. J. (2006) · Nature reviews. Cancer · doi:10.1038/nrc1840 · Cited by 7,038 · see citing works
Okano, M., Bell, D. W., Haber, D. A., & Li, E. (1999) · Cell · doi:10.1016/s0092-8674(00)81656-6 · Cited by 6,143 · see citing works
Derrien, T., Johnson, R., Bussotti, G., Andrea Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,017 · see citing works
Warde-Farley, D., Donaldson, S. L., Comes, O., Zuberi, K., Badrawi, R., Chao, P., Franz, M., Grouios, C., Kazi, F., Lopes, C. T., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq537 · Cited by 4,835 · see citing works
Kong, L., Zhang, Y., Ye, Z., Liu, X., Zhao, S.-Q., Wei, L., & Gao, G. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm391 · Cited by 2,773 · see citing works
microRNAs as oncogenes and tumor suppressors
Zhang, B., Pan, X., Cobb, G. P., & Anderson, T. A. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.028 · Cited by 2,755 · see citing works
Integration of biological networks and gene expression data using Cytoscape
Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., et al. (2007) · Nature Protocols · doi:10.1038/nprot.2007.324 · Cited by 2,507 · see citing works
Massive genomic rearrangement acquired in a single catastrophic event during cancer development
Stephens, P. J., Greenman, C. D., Fu, B., Yang, F., Bignell, G. R., Mudie, L. J., Pleasance, E. D., Lau, K. W., Beare, D., Stebbings, L. A., et al. (2011) · Cell · doi:10.1016/j.cell.2010.11.055 · Cited by 2,414 · see citing works
Oncogenic pathway signatures in human cancers as a guide to targeted therapies
Bild, A., Yao, G., Chang, J. T., Wang, Q., Potti, A., Chasse, D. A. D., Joshi, M.-B., Harpole, D. H., Lancaster, J. M., Berchuck, A., et al. (2005) · Nature · doi:10.1038/nature04296 · Cited by 1,992 · see citing works
Molecular classification of cutaneous malignant melanoma by gene expression profiling
Bittner, M. L., Meltzer, P. S., Chen, Y., Jiang, Y. Y., Seftor, E. A., Hendrix, M. J. C., Radmacher, M. D., Simon, R., Zohar Yakhini, B., Ben‐Dor, A., et al. (2000) · Nature · doi:10.1038/35020115 · Cited by 1,989 · see citing works
Fabbri, M., Garzon, R., Cimmino, A., Liu, Z., Zanesi, N. A. O., Callegari, E., Liu, S., Alder, H., Costinean, S., Fernandez-Cymering, C., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707628104 · Cited by 1,676 · 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
Saito, Y., Liang, G., Egger, G., Friedman, J. M., Chuang, J. C., Coetzee, G. A., & Jones, P. A. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.04.020 · Cited by 1,328 · see citing works
A tumorigenic subpopulation with stem cell properties in melanomas
Fang, D., Nguyen, T. K., Leishear, K., Finko, R., Kulp, A. N., Hotz, S., Van Belle, P. A., Xu, X., Elder, D. E., & Herlyn, M. (2005) · Cancer Research · doi:10.1158/0008-5472.can-05-1343 · Cited by 1,280 · see citing works
GOstat: find statistically overrepresented Gene Ontologies within a group of genes
Beißbarth, T., & Speed, T. P. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth088 · Cited by 1,256 · see citing works
DNA methylation and gene silencing in cancer
Baylin, S. B. (2005) · Nature Clinical Practice Oncology · doi:10.1038/ncponc0354 · Cited by 1,156 · see citing works
A microRNA DNA methylation signature for human cancer metastasis
Lujambio, A., Calin, G. A., Villanueva, A., Ropero, S., Sánchez‐Céspedes, M., Blanco, D., Montuenga, L. M., Rossi, S., Nicoloso, M. S., Faller, W. J., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803055105 · Cited by 1,078 · see citing works
Increased methylation variation in epigenetic domains across cancer types
Hansen, K. D., Timp, W., Bravo, H. C., Sabunciyan, S., Langmead, B., McDonald, O. G., Wen, B., Wu, H., Liu, Y., Diep, D. H., et al. (2011) · Nature Genetics · doi:10.1038/ng.865 · Cited by 1,053 · see citing works
microRNAs exhibit high frequency genomic alterations in human cancer
Zhang, L., Huang, J., Yang, N., Greshock, J. D., Megraw, M. S., Giannakakis, A., Liang, S., Naylor, T. L., Barchetti, A., Ward, M. R., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508889103 · Cited by 1,032 · see citing works
Genetic Unmasking of an Epigenetically Silenced microRNA in Human Cancer Cells
Lujambio, A., Ropero, S., Ballestar, E., Fraga, M. F., Cerrato, C., Setién, F., Casado, S., Suárez‐Gauthier, A., Sánchez‐Céspedes, M., Gitt, A., et al. (2007) · Cancer Research · doi:10.1158/0008-5472.can-06-4218 · Cited by 939 · see citing works
Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells
Bestor, T. H., Laudano, A. P., Mattaliano, R. J., & Ingram, V. M. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90122-2 · Cited by 913 · see citing works
The UCSC Genome Browser database: extensions and updates 2013
Meyer, L. R., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Kuhn, R. M., Wong, M., Sloan, C. A., Rosenbloom, K. R., Roe, G. R., Rhead, B. L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1048 · Cited by 901 · see citing works
Landscape of Somatic Retrotransposition in Human Cancers
Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L. J., Lohr, J. G., Harris, C. C., Ding, L., Wilson, R. K., et al. (2012) · Science · doi:10.1126/science.1222077 · Cited by 762 · see citing works
MicroRNAs as Oncogenes and Tumor Suppressors
Chen, C. (2005) · New England Journal of Medicine · doi:10.1056/nejmp058190 · Cited by 760 · see citing works
Melanoma genome sequencing reveals frequent PREX2 mutations
Berger, M. F., Hodis, E., Heffernan, T. P., Deribe, Y. L., Lawrence, M. S., Protopopov, A., Ivanova, E., Watson, I. R., Nickerson, E., Ghosh, P., et al. (2012) · Nature · doi:10.1038/nature11071 · Cited by 756 · see citing works
A small piece in the cancer puzzle: microRNAs as tumor suppressors and oncogenes
Kent, O. A., & Mendell, J. T. (2006) · Oncogene · doi:10.1038/sj.onc.1209913 · Cited by 715 · see citing works
MicroRNA function in cancer: oncogene or a tumor suppressor?
Shenouda, S. K., & Alahari, S. K. (2009) · Cancer and Metastasis Reviews · doi:10.1007/s10555-009-9188-5 · Cited by 677 · see citing works
miR-15a and miR-16-1 in cancer: discovery, function and future perspectives
Aqeilan, R. I., Calin, G. A., & Croce, C. M. (2009) · Cell Death and Differentiation · doi:10.1038/cdd.2009.69 · Cited by 650 · see citing works
Gaur, A., Jewell, D. A., Liang, Y., Ridzon, D., Moore, J. H., Chen, C., Ambros, V. R., & Israel, M. A. (2007) · Cancer Research · doi:10.1158/0008-5472.can-06-2698 · Cited by 593 · see citing works
lncRNAdb: a reference database for long noncoding RNAs
Amaral, P., Clark, M. B., Gascoigne, D. K., Dinger, M. E., & Mattick, J. S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1138 · Cited by 584 · see citing works
Self-citationSegura, M. F., Hanniford, D., Menéndez, S., Reavie, L. B., Zou, X., Álvarez-Díaz, S., Zakrzewski, J., Blochin, E., Rose, A. E., Bogunovic, D., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808263106 · Cited by 538 · see citing works
Expression Profiling Reveals Novel Pathways in the Transformation of Melanocytes to Melanomas
Hoek, K. S., Rimm, D. L., Williams, K. R., Zhao, H., Ariyan, S., Lin, A., Kluger, H. M., Berger, A. J., Cheng, E., Trombetta, E. S., et al. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-0731 · Cited by 478 · see citing works
DNA methylation and methyl-CpG binding proteins: developmental requirements and function
Bogdanović, O., & Veenstra, G. J. C. (2009) · Chromosoma · doi:10.1007/s00412-009-0221-9 · Cited by 474 · see citing works
Exome sequencing identifies GRIN2A as frequently mutated in melanoma
Program, N. C. S., Wei, X., Walia, V., Lin, J., Teer, J. K., Prickett, T. D., Gartner, J. J., Davis, S. R., Stemke‐Hale, K., Davies, M. A., et al. (2011) · Nature Genetics · doi:10.1038/ng.810 · Cited by 463 · see citing works
Epigenetic inactivation of microRNA gene hsa‐mir‐9‐1 in human breast cancer
Lehmann, U., Hasemeier, B., Christgen, M., Müller, M., Römermann, D., Länger, F. P., & Kreipe, H. H. (2007) · The Journal of Pathology · doi:10.1002/path.2251 · Cited by 460 · see citing works
Schultz, J., Lorenz, P., Gross, G., Ibrahim, S. M., & Kunz, M. (2008) · Cell Research · doi:10.1038/cr.2008.45 · Cited by 447 · see citing works
Houghton, A. N., & Polsky, D. (2002) · Cancer Cell · doi:10.1016/s1535-6108(02)00161-7 · Cited by 415 · see citing works
Expression profiling reveals novel pathways in the transformation of Melanocytes to Melanomas.
Hoek, K. S., Rimm, D. L., Williams, K. R., Zhao, H., Ariyan, S., Lin, A. J., Kluger, H. M., Berger, A. J., Cheng, E., Trombetta, E. S., et al. (2004) · Pigment Cell Research · doi:10.1111/j.1600-0749.2004.00175_12.x · Cited by 412 · see citing works
The roles of microRNA in cancer and apoptosis
Lynam‐Lennon, N., Maher, S. G., & Reynolds, J. V. (2008) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2008.00061.x · Cited by 408 · see citing works
Hammond, S. M. (2005) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2005.12.005 · Cited by 405 · see citing works
Serre, D., Lee, B. H., & Ting, A. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp992 · Cited by 404 · see citing works
Epigenetic Silencing of the Myelopoiesis Regulator microRNA-223 by the AML1/ETO Oncoprotein
Fazi, F., Racanicchi, S., Zardo, G., Starnes, L. M., Mancini, M., Travaglini, L., Diverio, D., Ammatuna, E., Cimino, G. G., Lo‐Coco, F., et al. (2007) · Cancer Cell · doi:10.1016/j.ccr.2007.09.020 · Cited by 381 · see citing works
Felicetti, F., Errico, M. C., Bottero, L., Segnalini, P., Stoppacciaro, A., Biffoni, M., Felli, N., Mattia, G., Petrini, M., Colombo, M. P., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-2538 · Cited by 378 · see citing works
MicroRNAs and the hallmarks of cancer
Dalmay, T., & Edwards, D. R. (2006) · Oncogene · doi:10.1038/sj.onc.1209911 · Cited by 368 · see citing works
DNA methylation regulates microRNA expression
Han, L., Witmer, P. D., Casey, E. R., Valle, D. L., & Sukumar, S. V. (2007) · Cancer Biology & Therapy · doi:10.4161/cbt.6.8.4486 · Cited by 333 · see citing works
Integrative analysis of the melanoma transcriptome
Berger, M. F., Levin, J. Z., Vijayendran, K., Sivachenko, A., Adiconis, X., Maguire, J., Johnson, L. A., Robinson, J., Verhaak, R. G., Sougnez, C., et al. (2010) · Genome Research · doi:10.1101/gr.103697.109 · Cited by 305 · see citing works
Increased expression of stem cell markers in malignant melanoma
Klein, W. M., Wu, B. P., Zhao, S., Wu, H. G., Klein–Szanto, A. J., & Tahan, S. R. (2006) · Modern Pathology · doi:10.1038/modpathol.3800720 · Cited by 304 · see citing works
Epigenetic silencing of the intronic microRNA hsa-miR-342 and its host gene EVL in colorectal cancer
Grady, W. M., Parkin, R. K., Mitchell, P. S., Lee, J. H., Kim, Y.-H., Tsuchiya, K. D., Washington, M. K., Paraskeva, C., Willson, J. K. V., Kaz, A. M., et al. (2008) · Oncogene · doi:10.1038/onc.2008.10 · Cited by 292 · see citing works
MicroRNA-137 Targets Microphthalmia-Associated Transcription Factor in Melanoma Cell Lines
Bemis, L., Chen, R., Amato, C. M., Classen, E. H., Robinson, S. E., Coffey, D. G., Erickson, P. F., Shellman, Y. G., & Robinson, W. A. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-2912 · Cited by 273 · see citing works
Mueller, D. W., Rehli, M., & Bosserhoff, A. (2009) · Journal of Investigative Dermatology · doi:10.1038/jid.2008.452 · Cited by 246 · see citing works
The Regulation of miRNA-211 Expression and Its Role in Melanoma Cell Invasiveness
Mazar, J., Deyoung, K. L., Khaitan, D., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013779 · Cited by 204 · see citing works
Self-citationDeep sequencing reveals distinct patterns of DNA methylation in prostate cancer
Kim, J. H., Dhanasekaran, S. M., Prensner, J. R., Cao, X., Robinson, D., Kalyana-Sundaram, S., Huang, C., Shankar, S., Jing, X., Iyer, M., et al. (2011) · Genome Research · doi:10.1101/gr.119347.110 · Cited by 188 · see citing works
CancerGenes: a gene selection resource for cancer genome projects
Higgins, M. E., Claremont, M., Major, J. E., Sander, C., & Lash, A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl811 · Cited by 179 · see citing works
Epigenetic Silencing of Novel Tumor Suppressors in Malignant Melanoma
Muthusamy, V., Duraisamy, S., Bradbury, C. M., Hobbs, C., Curley, D. P., Nelson, B., & Bosenberg, M. (2006) · Cancer Research · doi:10.1158/0008-5472.can-06-1274 · Cited by 170 · see citing works
Redefining CpG islands using hidden Markov models
Wu, H., Caffo, B. S., Jaffee, H. A., Irizarry, R. A., & Feinberg, A. P. (2010) · Biostatistics · doi:10.1093/biostatistics/kxq005 · Cited by 166 · see citing works
RNA Pol II Accumulates at Promoters of Growth Genes During Developmental Arrest
Baugh, L. R., DeModena, J. A., & Sternberg, P. W. (2009) · Science · doi:10.1126/science.1169628 · Cited by 165 · see citing works
Øster, B., Thorsen, K., Lamy, P., et al. (2011) · International Journal of Cancer · doi:10.1002/ijc.25951 · Cited by 156 · see citing works
Spugnardi, M., Tommasi, S., Dammann, R., Pfeifer, G. P., & Hoon, D. S. �. (2003) · PubMed · Cited by 153 · see citing works
Laminin-Induced Signaling in Tumor Cells
Givant-Horwitz, V., Davidson, B., & Reich, R. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-3424 · Cited by 151 · see citing works
EPD in its twentieth year: towards complete promoter coverage of selected model organisms
Schmid, C. D. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj146 · Cited by 132 · see citing works
MicroRNAs in the Search for Understanding Human Diseases
Perera, R. J., & Ray, A. (2007) · BioDrugs · doi:10.2165/00063030-200721020-00004 · Cited by 130 · see citing works
Self-citationRegulation of microRNA processing in development, differentiation and cancer
Schmittgen, T. D. (2008) · Journal of Cellular and Molecular Medicine · doi:10.1111/j.1582-4934.2008.00483.x · Cited by 110 · see citing works
Gene-expression profiling in human cutaneous melanoma
Carr, K. M., Bittner, M. L., & Trent, J. M. (2003) · Oncogene · doi:10.1038/sj.onc.1206448 · Cited by 102 · see citing works
MicroRNA-dependent regulation of cKit in cutaneous melanoma
Igoucheva, O., & Alexeev, V. Y. (2009) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2008.12.152 · Cited by 96 · see citing works
Epigenetic events in malignant melanoma
Rothhammer-Hampl, T., & Bosserhoff, A. (2007) · Pigment Cell Research · doi:10.1111/j.1600-0749.2007.00367.x · Cited by 95 · see citing works
Howell, P., Liu, S., Ren, S., Behlen, C., Fodstad, Ø., & Riker, A. I. (2009) · Cancer Control · doi:10.1177/107327480901600302 · Cited by 93 · see citing works
Shann, Y., Cheng, C., Chiao, C.-H., Chen, D.-T., Li, P.-H., & Hsu, M. (2008) · Genome Research · doi:10.1101/gr.070961.107 · Cited by 88 · see citing works
Epigenetic regulation of microRNA‐375 and its role in melanoma development in humans
Mazar, J., DeBlasio, D., Govindarajan, S. S., et al. (2011) · FEBS Letters · doi:10.1016/j.febslet.2011.06.025 · Cited by 86 · see citing works
Self-citationAberrant expression of miR‐196a in gastric cancers and correlation with recurrence
Tsai, K., Liao, Y., Wu, C., Hu, L., Li, S., Chan, W., Ho, M., Lai, C., Kao, H., Fang, W., et al. (2011) · Genes Chromosomes and Cancer · doi:10.1002/gcc.21924 · Cited by 82 · see citing works
DNA Methylation: Bisulphite Modification and Analysis
Patterson, K., Molloy, L., Qu, W., & Clark, S. J. (2011) · Journal of Visualized Experiments · doi:10.3791/3170 · Cited by 75 · see citing works
Yu, W., Jin, C., Lou, X., Han, X., Li, L., He, Y., Zhang, H., Ma, K., Zhu, J., Cheng, L., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0029450 · Cited by 74 · see citing works
MicroRNA-221 and -222 pathway controls melanoma progression
Felicetti, F., Errico, M. C., Segnalini, P., Mattia, G., & Carè, A. (2008) · Expert Review of Anticancer Therapy · doi:10.1586/14737140.8.11.1759 · Cited by 69 · see citing works
Mazar, J., Khaitan, D., DeBlasio, D., Zhong, C., Govindarajan, S. S., Kopanathi, S., Zhang, S., Ray, A., & Perera, R. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024922 · Cited by 65 · see citing works
Self-citationBízik, J., Lizonová, A., Stephens, R. W., et al. (1990) · Cell Regulation · doi:10.1091/mbc.1.12.895 · Cited by 45 · see citing works
Li, Z., Zhang, W., Shao, Y., et al. (2009) · Medical Oncology · doi:10.1007/s12032-009-9323-8 · Cited by 45 · see citing works
Chen, A., Luo, M., Yuan, G., Yu, J., Deng, T., Zhang, L., Zhou, Y., Mitchelson, K. R., & Cheng, J. (2008) · Biotechnology Letters · doi:10.1007/s10529-008-9800-8 · Cited by 45 · see citing works
DNA Binding of Methyl-CpG-Binding Protein MeCP2 in Human MCF7 Cells
Koch, C., & Strätling, W. H. (2004) · Biochemistry · doi:10.1021/bi0359271 · Cited by 33 · see citing works
Epigenetic Lesions in Malignant Melanoma
Schwabe, M., & Lübbert, M. (2007) · Current Pharmaceutical Biotechnology · doi:10.2174/138920107783018372 · Cited by 30 · see citing works
Epigenetic Regulation of miRNA Genes and their Role in Human Melanomas
Perera, R. J., & Ray, A. (2012) · Epigenomics · doi:10.2217/epi.11.114 · Cited by 29 · see citing works
Self-citationChatagnon, A., Perriaud, L., Nazaret, N., Croze, S., Benhattar, J., Lachuer, J., & Dante, R. (2011) · Epigenetics · doi:10.4161/epi.6.11.17875 · Cited by 28 · see citing works
Gomez-Sarosi, L., Strasberg–Rieber, M., & Rieber, M. (2009) · Cancer Biology & Therapy · doi:10.4161/cbt.8.12.8561 · Cited by 22 · see citing works
Coexpression of tumor‐associated α2‐macroglobulin and growth factors in human melanoma cell lines
Lizonová, A., Bízik, J., Grofova, M., et al. (1990) · Journal of Cellular Biochemistry · doi:10.1002/jcb.240430404 · Cited by 15 · see citing works
Loriot, A. E., Parvizi, G. K., Reister, S., et al. (2011) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2011.11.120 · Cited by 9 · see citing works
Alpha-2-macroglobulin is not synthesized by human urothelial cell lines in vitro.
Grofova, M., Bízik, J., Lizonová, A., et al. (1990) · PubMed · Cited by 2 · see citing works
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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
Giricz, O., Mo, Y., Dahlman, K. B., Cotto-Rios, X. M., Vardabasso, C., Nguyen, H., Matusow, B., Bartenstein, M., Polishchuk, V., Johnson, D. B., et al. (2018) · JCI Insight · doi:10.1172/jci.insight.120422 · Cited by 40 · see citing works
- Authors
- Li, J.-L., Mazar, J., Zhong, C., Faulkner, G. J., Govindarajan, S. S., Zhang, Z., Dinger, M. E., Meredith, G., Adams, C., Zhang, S., Mattick, J. S., Ray, A., & Perera, R. J.
- Affiliations
- Sanford Burnham Prebys Medical Discovery Institute (US)
- University of Central Florida (US)
- The University of Queensland (AU)
- Garvan Institute of Medical Research (AU)
- Keck Graduate Institute (US)
- Corresponding author
- Ray, Animesh
- Perera, Ranjan J.
- ORCID
- Venue
- Scientific Reports
- Published
- 2013-10-16
- Volume
- 3
- Issue
- 1
- Pages
- 2962-2962
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC3797435
- OpenAlex
- W2061105371
- Cited by
- 21
- References
- 89
- Citations by year
- 2026: 1 · 2024: 2 · 2022: 2 · 2020: 1 · 2019: 1 · 2018: 3 · 2017: 2 · 2016: 3 · 2015: 4 · 2014: 2
- FWCI
- 1.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Journal of International Crisis and Risk Communication Research (submittedVersion)
- Funders
- National Science Foundation (0527023)
- Life Technologies Corporation
- CHDI Foundation
- National Institutes of Health
- National Cancer Institute (R03CA165184)
- National Institute of General Medical Sciences (R01GM084881)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- melanoma, DNA methylation, CpG islands, differentially methylated regions, epigenetics, co-expression network, TERC, telomerase RNA, LTR retrotransposons, non-coding RNA, gene expression regulation, metastatic melanoma
- MeSH terms
- Humans, Melanoma, Repetitive Sequences, Nucleic Acid, Gene Expression Regulation, Neoplastic, Cluster Analysis, CpG Islands, DNA Methylation, Gene Expression Profiling, Gene Order, Epigenesis, Genetic, Cell Line, Tumor, Gene Regulatory Networks, Genome-Wide Association Study
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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