tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation

被引:0
|
作者
Chambaz, Antoine [1 ]
Neuvial, Pierre [2 ]
机构
[1] Univ Paris Ouest Nanterre, ModalX, Nanterre, France
[2] Univ Evry val Essonne, Lab Math & Modelisat Evry, CNRS, ENSIIE,USC INRA,UMR 8071, Evry, France
关键词
D O I
10.1093/bioinformatics/btv320
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
We describe the implementation of the method introduced by Chambaz et al. in 2012. We also demonstrate its genome-wide application to the integrative search of new regions with strong association between DNA copy number and gene expression accounting for DNA methylation in breast cancers.
引用
收藏
页码:3054 / 3056
页数:3
相关论文
共 50 条
  • [1] Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse
    Krzeminski, Patryk
    Corchete, Luis A.
    Garcia, Juan L.
    Lopez-Corral, Lucia
    Ferminan, Encarna
    Garcia, Eva M.
    Martin, Ana A.
    Hernandez-Rivas, Jesus M.
    Garcia-Sanz, Ramon
    San Miguel, Jesus F.
    Gutierrez, Norma C.
    [J]. ONCOTARGET, 2016, 7 (49) : 80664 - 80679
  • [2] INTEGRATIVE ANALYSIS OF DNA COPY NUMBER, DNA METHYLATION AND GENE EXPRESSION IN MULTIPLE MYELOMA REVEALS ALTERATIONS RELATED TO RELAPSE
    Krzeminski, P.
    Corchete, L.
    Martin, A.
    Lopez-Corral, L. L. C.
    Ferminan, E.
    Garcia, E.
    Garcia, J. L.
    Hernandez-Rivas, J.
    Garcia-Sanz, R.
    Miguel, J. San
    Gutierrez, N.
    [J]. HAEMATOLOGICA, 2016, 101 : 517 - 517
  • [3] The association between copy number aberration, DNA methylation and gene expression in tumor samples
    Sun, Wei
    Bunn, Paul
    Jin, Chong
    Little, Paul
    Zhabotynsky, Vasyl
    Perou, Charles M.
    Hayes, David Neil
    Chen, Mengjie
    Lin, Dan-Yu
    [J]. NUCLEIC ACIDS RESEARCH, 2018, 46 (06) : 3009 - 3018
  • [4] Integrative analysis of gene mutations, copy number alterations and DNA methylation in colorectal serrated lesions
    Sawada, Takeshi
    Nakanishi, Hiroyoshi
    Sasaki, Yasushi
    Yamamoto, Eiichiro
    Aoki, Hironori
    Eizuka, Makoto
    Takahashi, Naoki
    Ota, Ryosuke
    Kubota, Eiji
    Kataoka, Hiromi
    Minamoto, Toshinari
    Sugai, Tamotsu
    Suzuki, Hiromu
    [J]. CANCER SCIENCE, 2018, 109 : 1157 - 1157
  • [5] Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes
    Lee, Hyunju
    Kong, Sek Won
    Park, Peter J.
    [J]. BIOINFORMATICS, 2008, 24 (07) : 889 - 896
  • [6] Association between sperm mitochondarial DNA copy number and nuclear DNA methylation
    Oluwayiose, Oladele A.
    Josyula, Srinihaari
    Houle, Emily
    Marcho, Chelsea
    Whitcomb, Brian W.
    Rahil, Tayyab
    Sites, Cynthia K.
    Pilsner, J. Richard
    [J]. EPIGENOMICS, 2020, 12 (24) : 2141 - 2153
  • [7] Integrative analyses of gene expression, DNA methylation, genotype and copy number alterations characterize X-chromosome inactivation in ovarian cancer
    Winham, Stacey J.
    Larson, Nicholas B.
    Armasu, Sebastian M.
    Fogarty, Zachary C.
    Larson, Melissa C.
    Kalli, Kimberly R.
    Lawrenson, Kate
    Gayther, Simon
    Fridley, Brooke L.
    Goode, Ellen L.
    [J]. CANCER RESEARCH, 2017, 77
  • [8] Quantitation of DNA methylation and copy number variations by targeted sequencing of retrotransposon.
    Buis, Jeffrey
    Goodman, Tom
    Kim, Julie
    Kruger, Adele
    Tarrier, Brendan
    Ma, Jie
    Stoerker, Jay
    [J]. JOURNAL OF CLINICAL ONCOLOGY, 2016, 34 (15)
  • [9] Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review
    Lahti, Leo
    Schaefer, Martin
    Klein, Hans-Ulrich
    Bicciato, Silvio
    Dugas, Martin
    [J]. BRIEFINGS IN BIOINFORMATICS, 2013, 14 (01) : 27 - 35
  • [10] Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours
    Sun, Xin
    St John, Justin C.
    [J]. EPIGENETICS & CHROMATIN, 2018, 11