Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia

[1]  S. Rajalakshmi,et al.  5-azacytidine potentiates initiation induced by carcinogens in rat liver. , 1985, Carcinogenesis.

[2]  A. Feinberg,et al.  Reduced genomic 5-methylcytosine content in human colonic neoplasia. , 1988, Cancer research.

[3]  Rui Luo,et al.  Is My Network Module Preserved and Reproducible? , 2011, PLoS Comput. Biol..

[4]  Anthony P. Fejes,et al.  Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. , 2008, Genome research.

[5]  K. Zhao,et al.  Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle , 2013, PLoS genetics.

[6]  Lisa L. Smith,et al.  Epigenetic Profiling in Chronic Lymphocytic Leukemia Reveals Novel Methylation Targets , 2004, Cancer Research.

[7]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[8]  Timothy J. Durham,et al.  "Systematic" , 1966, Comput. J..

[9]  John Calvin Reed,et al.  bcl-2 gene hypomethylation and high-level expression in B-cell chronic lymphocytic leukemia. , 1993, Blood.

[10]  Robert Gentleman,et al.  Using GOstats to test gene lists for GO term association , 2007, Bioinform..

[11]  L. Alhonen,et al.  Genomic hypomethylation in human chronic lymphocytic leukemia. , 1992, Blood.

[12]  Mikhail G. Dozmorov,et al.  GenomeRunner: automating genome exploration , 2012, Bioinform..

[13]  Peter W. Laird,et al.  DNA Hypomethylation and Ovarian Cancer Biology , 2004, Cancer Research.

[14]  A. Giuliano,et al.  Global DNA hypomethylation increases progressively in cervical dysplasia and carcinoma , 1994, Cancer.

[15]  Jiangwen Zhang,et al.  Genome-wide lineage-specific transcriptional networks underscore Ikaros-dependent lymphoid priming in hematopoietic stem cells. , 2009, Immunity.

[16]  L. Alhonen,et al.  Hypomethylation of ornithine decarboxylase gene and erb-A1 oncogene in human chronic lymphatic leukemia. , 1988, Blood.

[17]  Hanna Göransson,et al.  Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia. , 2010, Blood.

[18]  Tsviya Olender,et al.  GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation. , 2009, Omics : a journal of integrative biology.

[19]  Wendy A Bickmore,et al.  Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes , 2013, Genome Biology.

[20]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[21]  A. Feinberg,et al.  Hypomethylation distinguishes genes of some human cancers from their normal counterparts , 1983, Nature.

[22]  J. S. Rao,et al.  Demethylation-linked activation of urokinase plasminogen activator is involved in progression of prostate cancer. , 2007, Cancer research.

[23]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[24]  M. Ehrlich,et al.  Satellite DNA hypomethylation vs. overall genomic hypomethylation in ovarian epithelial tumors of different malignant potential. , 1999, Mutation research.

[25]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[26]  S. Vandenberg,et al.  Genome-wide hypomethylation in human glioblastomas associated with specific copy number alteration, methylenetetrahydrofolate reductase allele status, and increased proliferation. , 2006, Cancer research.

[27]  Thierry Boon,et al.  DNA Methylation Is the Primary Silencing Mechanism for a Set of Germ Line- and Tumor-Specific Genes with a CpG-Rich Promoter , 1999, Molecular and Cellular Biology.

[28]  V. Speights,et al.  Global hypomethylation is common in prostate cancer cells: a quantitative predictor for clinical outcome? , 2005, Cancer genetics and cytogenetics.

[29]  D. Weisenburger,et al.  Downregulation of Death-Associated Protein Kinase 1 (DAPK1) in Chronic Lymphocytic Leukemia , 2007, Cell.

[30]  M. Grever,et al.  TWIST2 demonstrates differential methylation in immunoglobulin variable heavy chain mutated and unmutated chronic lymphocytic leukemia. , 2005, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[31]  M. Widschwendter,et al.  DNA hypomethylation is prevalent even in low-grade breast cancers , 2004, Cancer biology & therapy.

[32]  J. Byrd,et al.  CpG island methylation and expression of the secreted frizzled-related protein gene family in chronic lymphocytic leukemia. , 2006, Cancer research.

[33]  Alfonso Valencia,et al.  Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia , 2012, Nature Genetics.

[34]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[35]  Ramin Massoumi,et al.  Cyld Inhibits Tumor Cell Proliferation by Blocking Bcl-3-Dependent NF-κB Signaling , 2006, Cell.

[36]  Francine E. Garrett-Bakelman,et al.  methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.

[37]  Jing-Dong J Han,et al.  Evolution of Alu elements toward enhancers. , 2014, Cell reports.

[38]  Emili Montserrat,et al.  ZAP-70 expression as a surrogate for immunoglobulin-variable-region mutations in chronic lymphocytic leukemia. , 2003, The New England journal of medicine.

[39]  P. Laird,et al.  Hypomethylation and hypermethylation of DNA in Wilms tumors , 2002, Oncogene.

[40]  Felix Krueger,et al.  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..

[41]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[42]  N. Chiorazzi,et al.  Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. , 1999, Blood.

[43]  Hengbin Wang,et al.  Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing , 2002, Science.

[44]  M. Yano,et al.  Human Werner helicase interacting protein 1 (WRNIP1) functions as a novel modulator for DNA polymerase δ , 2004, Genes to cells : devoted to molecular & cellular mechanisms.

[45]  S. S. Ajay,et al.  Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites , 2012, Genome research.

[46]  Guillaume J. Filion,et al.  A Family of Human Zinc Finger Proteins That Bind Methylated DNA and Repress Transcription , 2006, Molecular and Cellular Biology.

[47]  Meng Li,et al.  Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer , 2009, BMC Medical Genomics.

[48]  N. Chiorazzi,et al.  B cell chronic lymphocytic leukemia: lessons learned from studies of the B cell antigen receptor. , 2003, Annual review of immunology.

[49]  Derek A. West,et al.  Silencing of the inhibitor of DNA binding protein 4 (ID4) contributes to the pathogenesis of mouse and human CLL. , 2011, Blood.

[50]  G. Nolan,et al.  The candidate proto-oncogene bcl-3 encodes a transcriptional coactivator that activates through NF-kappa B p50 homodimers. , 1993, Genes & development.

[51]  L. Vives,et al.  Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells , 2007, Nucleic acids research.

[52]  D. Reinberg,et al.  Processing the H3K36me3 signature , 2009, Nature Genetics.

[53]  Y. Liaw,et al.  Genome-wide hypomethylation in hepatocellular carcinogenesis. , 2001, Cancer research.

[54]  M. Szyf,et al.  Pharmacological inhibition of DNA methylation induces proinvasive and prometastatic genes in vitro and in vivo. , 2008, Neoplasia.

[55]  Jun Qin,et al.  Purification and functional characterization of the human N‐CoR complex: the roles of HDAC3, TBL1 and TBLR1 , 2003, The EMBO journal.

[56]  O. Galm,et al.  CpG island methylation patterns in chronic lymphocytic leukemia , 2009, Leukemia & lymphoma.

[57]  David F. Kashatus,et al.  Expression of the Bcl-3 proto-oncogene suppresses p53 activation. , 2006, Genes & development.

[58]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[59]  T J Hamblin,et al.  Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia. , 1999, Blood.

[60]  R. Hazan,et al.  Cadherin Switch in Tumor Progression , 2004, Annals of the New York Academy of Sciences.

[61]  J. Hagman,et al.  B lymphocyte lineage specification, commitment and epigenetic control of transcription by early B cell factor 1. , 2012, Current topics in microbiology and immunology.

[62]  David E. Muench,et al.  c-Myc and Cancer Metabolism , 2012, Clinical Cancer Research.

[63]  J. Gribben How I treat CLL up front. , 2010, Blood.