Identification of epigenetically altered genes and potential gene targets in melanoma using bioinformatic methods

References

• KoJMFisherDEA new era: melanoma genetics and therapeuticsJ Pathol20112232242251
   Web of Science ®Google Scholar
• GludMGniadeckiRMicroRNAs in the pathogenesis of malignant melanomaJ Eur Acad Dermatol Venereol201327214215022621697
   PubMed Web of Science ®Google Scholar
• HillVKGartnerJJSamuelsYGoldsteinAMThe genetics of melanoma: recent advancesAnnu Rev Genomics Hum Genet20131425727923875803
   PubMed Web of Science ®Google Scholar
• PoynterJNElderJTFullenDRBRAF and NRAS mutations in melanoma and melanocytic neviMelanoma Res200616426727316845322
   PubMed Web of Science ®Google Scholar
• BirdADNA methylation patterns and epigenetic memoryGenes Dev200216162111782440
   PubMed Web of Science ®Google Scholar
• SigalottiLCovreAFrattaEEpigenetics of human cutaneous melanoma: setting the stage for new therapeutic strategiesJ Transl Med201085620540720
   PubMed Web of Science ®Google Scholar
• FreedbergDERigasSHRussakJFrequent p16-independent inactivation of p14ARF in human melanomaJ Natl Cancer Inst20081001178479518505964
   PubMedGoogle Scholar
• TommasiSZhengALiAXWuXBesratiniaAGene Expression Omnibus; Series GSE31879 Available at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31879Accessed November 15, 2017
   Google Scholar
• ZahurakMParmigianiGYuWPre-processing Agilent microarray dataBMC Bioinformatics20078114217472750
   PubMed Web of Science ®Google Scholar
• RitchieMEPhipsonBWuDLimma powers differential expression analyses for RNA-sequencing and microarray studiesNucleic Acids Res2015437e4725605792
   PubMed Web of Science ®Google Scholar
• SmythGKLimma: linear models for microarray dataGentlemanRCareyVDudoitSRIrizarryWHBioinformatics and computational biology solutions Using R and BioconductorNew YorkSpringer2005397420
   Google Scholar
• Consortium GOGene ontology consortium: going forwardNucleic Acids Res201543D1D1049D105625428369
   PubMed Web of Science ®Google Scholar
• KanehisaMSatoYKawashimaMFurumichiMTanabeMKEGG as a reference resource for gene and protein annotationNucleic Acids Res201644D1D457D46226476454
   PubMed Web of Science ®Google Scholar
• Huang daWShermanBTLempickiRASystematic and integrative analysis of large gene lists using DAVID bioinformatics resourcesNat Protoc200941445719131956
   PubMed Web of Science ®Google Scholar
• WuTAn accurate computation of the hypergeometric distribution functionACM Trans Math Software19931913343
   Web of Science ®Google Scholar
• KarolchikDBarberGPCasperJThe UCSC genome browser database: 2014 updateNucleic Acids Res201442D1D764D77024270787
   PubMed Web of Science ®Google Scholar
• RakosyZEcsediSTothRIntegrative genomics identifies gene signature associated with melanoma ulcerationPLoS One201381e5495823383013
   PubMed Web of Science ®Google Scholar
• EstellerMEpigenetics in cancerN Engl J Med2008358111148115918337604
   PubMed Web of Science ®Google Scholar
• De CarvalhoDDSharmaSYouJSDNA methylation screening identifies driver epigenetic events of cancer cell survivalCancer Cell201221565566722624715
   PubMed Web of Science ®Google Scholar
• BienvenuTPoirierKFriocourtGARX, a novel Prd-class-homeobox gene highly expressed in the telencephalon, is mutated in X-linked mental retardationHum Mol Genet200211898199111971879
   PubMed Web of Science ®Google Scholar
• FriocourtGKanataniSTabataHCell-autonomous roles of ARX in cell proliferation and neuronal migration during corticogenesisJ Neurosci200828225794580518509041
   PubMed Web of Science ®Google Scholar
• MarzeseDMScolyerRARoquéMDNA methylation and gene deletion analysis of brain metastases in melanoma patients identifies mutually exclusive molecular alterationsNeuro Oncol201416111499150924968695
   PubMed Web of Science ®Google Scholar
• MarzeseDMScolyerRAHuynhJLEpigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosisHum Mol Genet201423122623824014427
   PubMed Web of Science ®Google Scholar
• PujolsLMullolJPicadoCImportance of glucocorticoid receptors in upper and lower airwaysFront Biosci (Landmark Ed)200915789800
   Web of Science ®Google Scholar
• BhakooHSMilhollandRJLopezRKarakousisCRosenFHigh incidence and characterization of glucocorticoid receptors in human malignant melanoma 2, 3J Natl Cancer Inst198166121256935461
   PubMedGoogle Scholar
• DobosJKenesseyITímárJLadányiAGlucocorticoid receptor expression and antiproliferative effect of dexamethasone on human melanoma cellsPathol Oncol Res201117372973421455635
   PubMed Web of Science ®Google Scholar
• StoyanovaTRoyNKopanjaDBagchiSRaychaudhuriPDDB2 decides cell fate following DNA damageProc Natl Acad Sci USA200910626106901069519541625
   PubMed Web of Science ®Google Scholar
• LuijsterburgMSLindhMAcsKDDB2 promotes chromatin decondensation at UV-induced DNA damageJ Cell Biol2012197226728122492724
   PubMed Web of Science ®Google Scholar
• ItohTIwashitaSCohenMBMeyerholzDKLinnSDdb2 is a haploinsufficient tumor suppressor and controls spontaneous germ cell apoptosisHum Mol Genet200716131578158617468495
   PubMed Web of Science ®Google Scholar
• WangSQSetlowRBerwickMUltraviolet A and melanoma: a reviewJ Am Acad Dermatol200144583784611312434
   PubMed Web of Science ®Google Scholar
• HurlstoneAWellbrockCTP53 in the UV spotlight: a bona fide driver of melanomaPigment Cell Melanoma Res20142761010101125102761
   PubMed Web of Science ®Google Scholar
• NicholsAFItohTZolezziFHutsellSLinnSBasal transcriptional regulation of human damage-specific DNA-binding protein genes DDB1 and DDB2 by Sp1, E2F, N-myc and NF1 elementsNucleic Acids Res200331256256912527763
   PubMed Web of Science ®Google Scholar
• RenBCamHTakahashiYE2F integrates cell cycle progression with DNA repair, replication, and G2/M checkpointsGenes Dev200216224525611799067
   PubMed Web of Science ®Google Scholar
• PearsonGRobinsonFBeers GibsonTMitogen-activated protein (MAP) kinase pathways: regulation and physiological functions 1Endocr Rev200122215318311294822
   PubMed Web of Science ®Google Scholar
• FecherLAAmaravadiRKFlahertyKTThe MAPK pathway in melanomaCurr Opin Oncol200820218318918300768
   PubMed Web of Science ®Google Scholar
• RevestJ-MDi BlasiFKitchenerPThe MAPK pathway and Egr-1 mediate stress-related behavioral effects of glucocorticoidsNat Neurosci20058566415834420
   PubMed Web of Science ®Google Scholar
• Zöchbauer-MüllerSMinnaJDGazdarAFAberrant DNA methylation in lung cancer: biological and clinical implicationsOncologist20027545145712401908
   PubMed Web of Science ®Google Scholar
• WangWSrivastavaSStrategic approach to validating methylated genes as biomarkers for breast cancerCancer Prev Res2010311624
   Web of Science ®Google Scholar