1
|
Ettinger DS, Wood DE, Akerley W, Bazhenova
LA, Camidge DR, Cheney RT, Chirieac LR, D'Amico TA, Dilling TJ,
Dobelbower MC, et al: NCCN Guidelines Insights: Non-small cell lung
cancer, version 4.2016. J Natl Compr Canc Netw. 14:255–264. 2016.
View Article : Google Scholar : PubMed/NCBI
|
2
|
Sandoval J, Mendez-Gonzalez J, Nadal E,
Chen G, Carmona FJ, Sayols S, Moran S, Heyn H, Vizoso M, Gomez A,
et al: A prognostic DNA methylation signature for stage I
non-small-cell lung cancer. J Clin Oncol. 31:4140–4147. 2013.
View Article : Google Scholar : PubMed/NCBI
|
3
|
Cancer Genome Atlas Research Network.
Comprehensive molecular profiling of lung adenocarcinoma. Nature.
511:543–550. 2014. View Article : Google Scholar : PubMed/NCBI
|
4
|
Tang H, Xiao G, Behrens C, Schiller J,
Allen J, Chow CW, Suraokar M, Corvalan A, Mao J, White MA, et al: A
12-gene set predicts survival benefits from adjuvant chemotherapy
in non-small cell lung cancer patients. Clin Cancer Res.
19:1577–1586. 2013. View Article : Google Scholar : PubMed/NCBI
|
5
|
Karlsson A, Jönsson M, Lauss M, Brunnström
H, Jönsson P, Borg Å, Jönsson G, Ringnér M, Planck M and Staaf J:
Genome-wide DNA methylation analysis of lung carcinoma reveals one
neuroendocrine and four adenocarcinoma epitypes associated with
patient outcome. Clin Cancer Res. 20:6127–6140. 2014. View Article : Google Scholar : PubMed/NCBI
|
6
|
Rodríguez-Paredes M and Esteller M: Cancer
epigenetics reaches mainstream oncology. Nat Med. 17:330–339. 2011.
View Article : Google Scholar : PubMed/NCBI
|
7
|
Issa JP: DNA methylation as a clinical
marker in oncology. J Clin Oncol. 30:2566–2568. 2012. View Article : Google Scholar : PubMed/NCBI
|
8
|
Mehta A, Dobersch S, Romero-Olmedo AJ and
Barreto G: Epigenetics in lung cancer diagnosis and therapy. Cancer
Metastasis Rev. 34:229–241. 2015. View Article : Google Scholar : PubMed/NCBI
|
9
|
Selamat SA, Chung BS, Girard L, Zhang W,
Zhang Y, Campan M, Siegmund KD, Koss MN, Hagen JA, Lam WL, et al:
Genome-scale analysis of DNA methylation in lung adenocarcinoma and
integration with mRNA expression. Genome Res. 22:1197–1211. 2012.
View Article : Google Scholar : PubMed/NCBI
|
10
|
Mansfield AS, Wang L, Cunningham JM, Jen
J, Kolbert CP, Sun Z and Yang P: DNA methylation and RNA expression
profiles in lung adenocarcinomas of never-smokers. Cancer Genet.
208:253–260. 2015. View Article : Google Scholar : PubMed/NCBI
|
11
|
Robles AI, Arai E, Mathé EA, Okayama H,
Schetter AJ, Brown D, Petersen D, Bowman ED, Noro R, Welsh JA, et
al: An integrated prognostic classifier for stage I lung
adenocarcinoma based on mRNA, microRNA, and DNA methylation
biomarkers. J Thorac Oncol. 10:1037–1048. 2015. View Article : Google Scholar : PubMed/NCBI
|
12
|
Johnson WE, Li C and Rabinovic A:
Adjusting batch effects in microarray expression data using
empirical Bayes methods. Biostatistics. 8:118–127. 2007. View Article : Google Scholar : PubMed/NCBI
|
13
|
Sun Z, Chai HS, Wu Y, White WM, Donkena
KV, Klein CJ, Garovic VD, Therneau TM and Kocher JP: Batch effect
correction for genome-wide methylation data with illumina infinium
platform. BMC Med Genomics. 4:842011. View Article : Google Scholar : PubMed/NCBI
|
14
|
Team RC: R, . A language and environment
for statistical computing. R Foundation for Statistical Computing;
Vienna, Austria: https://www.R-project.org/2016
|
15
|
Du P, Zhang X, Huang CC, Jafari N, Kibbe
WA, Hou L and Lin SM: Comparison of Beta-value and M-value methods
for quantifying methylation levels by microarray analysis. BMC
Bioinformatics. 11:5872010. View Article : Google Scholar : PubMed/NCBI
|
16
|
Yin AA, Lu N, Etcheverry A, Aubry M,
Barnholtz-Sloan J, Zhang LH, Mosser J, Zhang W, Zhang X, Liu YH and
He YL: A novel prognostic six-CpG signature in glioblastomas. CNS
Neurosci Ther. 24:167–177. 2018. View Article : Google Scholar : PubMed/NCBI
|
17
|
Zhang XQ, Sun S, Lam KF, Kiang KM, Pu JK,
Ho AS, Lui WM, Fung CF, Wong TS and Leung GK: A long non-coding RNA
signature in glioblastoma multiforme predicts survival. Neurobiol
Dis. 58:123–131. 2013. View Article : Google Scholar : PubMed/NCBI
|
18
|
Huang DW, Sherman BT and Lempicki RA:
Systematic and integrative analysis of large gene lists using DAVID
bioinformatics resources. Nat Protoc. 4:44–57. 2009. View Article : Google Scholar : PubMed/NCBI
|
19
|
Mi H, Huang X, Muruganujan A, Tang H,
Mills C, Kang D and Thomas PD: PANTHER version 11: Expanded
annotation data from Gene Ontology and Reactome pathways, and data
analysis tool enhancements. Nucleic Acids Res. 45:D183–D189. 2017.
View Article : Google Scholar : PubMed/NCBI
|
20
|
BioCarta Pathways, . http://www.biocarta.com/March. 2016
|
21
|
KEGG, . Kyoto encyclopedia of genes and
genomes. https://www.genome.jp/kegg/Release 77.1.
2016
|
22
|
Hothorn T and Zeileis A: Generalized
maximally selected statistics. Biometrics. 64:1263–1269. 2008.
View Article : Google Scholar : PubMed/NCBI
|
23
|
Heller G, Zielinski CC and
Zöchbauer-Müller S: Lung cancer: From single-gene methylation to
methylome profiling. Cancer Metastasis Rev. 29:95–107. 2010.
View Article : Google Scholar : PubMed/NCBI
|
24
|
Brock MV, Hooker CM, Ota-Machida E, Han Y,
Guo M, Ames S, Glöckner S, Piantadosi S, Gabrielson E, Pridham G,
et al: DNA methylation markers and early recurrence in stage I lung
cancer. N Engl J Med. 358:1118–1128. 2008. View Article : Google Scholar : PubMed/NCBI
|
25
|
Burbee DG, Forgacs E, Zöchbauer-Müller S,
Shivakumar L, Fong K, Gao B, Randle D, Kondo M, Virmani A, Bader S,
et al: Epigenetic inactivation of RASSF1A in lung and breast
cancers and malignant phenotype suppression. J Natl Cancer Inst.
93:691–699. 2001. View Article : Google Scholar : PubMed/NCBI
|
26
|
Esteller M, Corn PG, Baylin SB and Herman
JG: A gene hypermethylation profile of human cancer. Cancer Res.
61:3225–3229. 2001.PubMed/NCBI
|
27
|
Virmani AK, Rathi A, Sathyanarayana UG,
Padar A, Huang CX, Cunnigham HT, Farinas AJ, Milchgrub S, Euhus DM,
Gilcrease M, et al: Aberrant methylation of the adenomatous
polyposis coli (APC) gene promoter 1A in breast and lung
carcinomas. Clin Cancer Res. 7:1998–2004. 2001.PubMed/NCBI
|
28
|
Heyn H and Esteller M: DNA methylation
profiling in the clinic: Applications and challenges. Nat Rev
Genet. 13:679–692. 2012. View Article : Google Scholar : PubMed/NCBI
|
29
|
Zhang X, Sun S, Pu JK, Tsang AC, Lee D,
Man VO, Lui WM, Wong ST and Leung GK: Long non-coding RNA
expression profiles predict clinical phenotypes in glioma.
Neurobiol Dis. 48:1–8. 2012. View Article : Google Scholar : PubMed/NCBI
|
30
|
Pfeifer GP and Rauch TA: DNA methylation
patterns in lung carcinomas. Semin Cancer Biol. 19:181–187. 2009.
View Article : Google Scholar : PubMed/NCBI
|
31
|
Diaz-Lagares A, Mendez-Gonzalez J, Hervas
D, Saigi M, Pajares MJ, Garcia D, Crujerias AB, Pio R, Montuenga
LM, Zulueta J, et al: A novel epigenetic signature for early
diagnosis in lung cancer. Clin Cancer Res. 22:3361–3371. 2016.
View Article : Google Scholar : PubMed/NCBI
|
32
|
Guo S, Yan F, Xu J, Bao Y, Zhu J, Wang X,
Wu J, Li Y, Pu W, Liu Y, et al: Identification and validation of
the methylation biomarkers of non-small cell lung cancer (NSCLC).
Clin Epigenetics. 7:32015. View Article : Google Scholar : PubMed/NCBI
|
33
|
Heller G, Altenberger C, Schmid B, Marhold
M, Tomasich E, Ziegler B, Müllauer L, Minichsdorfer C, Lang G,
End-Pfützenreuter A, et al: DNA methylation transcriptionally
regulates the putative tumor cell growth suppressor ZNF677 in
non-small cell lung cancers. Oncotarget. 6:394–408. 2015.
View Article : Google Scholar : PubMed/NCBI
|
34
|
Wrangle J, Machida EO, Danilova L, Hulbert
A, Franco N, Zhang W, Glöckner SC, Tessema M, Van Neste L, Easwaran
H, et al: Functional identification of cancer-specific methylation
of CDO1, HOXA9, and TAC1 for the diagnosis of lung cancer. Clin
Cancer Res. 20:1856–1864. 2014. View Article : Google Scholar : PubMed/NCBI
|
35
|
Brait M, Ling S, Nagpal JK, Chang X, Park
HL, Lee J, Okamura J, Yamashita K, Sidransky D and Kim MS: Cysteine
dioxygenase 1 is a tumor suppressor gene silenced by promoter
methylation in multiple human cancers. PLoS One. 7:e449512012.
View Article : Google Scholar : PubMed/NCBI
|
36
|
Li N and Li S: Epigenetic inactivation of
SOX1 promotes cell migration in lung cancer. Tumour Biol.
36:4603–4610. 2015. View Article : Google Scholar : PubMed/NCBI
|
37
|
Yin D, Jia Y, Yu Y, Brock MV, Herman JG,
Han C, Su X, Liu Y and Guo M: SOX17 methylation inhibits its
antagonism of Wnt signaling pathway in lung cancer. Discov Med.
14:33–40. 2012.PubMed/NCBI
|
38
|
Yin A, Etcheverry A, He Y, Aubry M,
Barnholtz-Sloan J, Zhang L, Mao X, Chen W, Liu B, Zhang W, et al:
Integrative analysis of novel hypomethylation and gene expression
signatures in glioblastomas. Oncotarget. 8:89607–89619. 2017.
View Article : Google Scholar : PubMed/NCBI
|
39
|
Devaney JM, Wang S, Funda S, Long J,
Taghipour DJ, Tbaishat R, Furbert-Harris P, Ittmann M and
Kwabi-Addo B: Identification of novel DNA-methylated genes that
correlate with human prostate cancer and high-grade prostatic
intraepithelial neoplasia. Prostate Cancer Prostatic Dis.
16:292–300. 2013. View Article : Google Scholar : PubMed/NCBI
|
40
|
Fang WJ, Zheng Y, Wu LM, Ke QH, Shen H,
Yuan Y and Zheng SS: Genome-wide analysis of aberrant DNA
methylation for identification of potential biomarkers in
colorectal cancer patients. Asian Pac J Cancer Prev. 13:1917–1921.
2012. View Article : Google Scholar : PubMed/NCBI
|
41
|
Litovkin K, Joniau S, Lerut E, Laenen A,
Gevaert O, Spahn M, Kneitz B, Isebaert S, Haustermans K, Beullens
M, et al: Methylation of PITX2, HOXD3, RASSF1 and TDRD1 predicts
biochemical recurrence in high-risk prostate cancer. J Cancer Res
Clin Oncol. 140:1849–1861. 2014. View Article : Google Scholar : PubMed/NCBI
|
42
|
Shaoqiang C, Yue Z, Yang L, Hong Z, Lina
Z, Da P and Qingyuan Z: Expression of HOXD3 correlates with shorter
survival in patients with invasive breast cancer. Clin Exp
Metastasis. 30:155–163. 2013. View Article : Google Scholar : PubMed/NCBI
|
43
|
Ye Q, Ding SF, Wang ZA, Feng J and Tan WB:
Influence of ribosomal protein L39-L in the drug resistance
mechanisms of lacrimal gland adenoid cystic carcinoma cells. Asian
Pac J Cancer Prev. 15:4995–5000. 2014. View Article : Google Scholar : PubMed/NCBI
|
44
|
Liu HS, Tan WB, Yang N, Yang YY, Cheng P,
Liu LJ, Wang WJ and Zhu CL: Effects of ribosomal protein l39-L on
the drug resistance mechanisms of lung cancer A549 cells. Asian Pac
J Cancer Prev. 15:3093–3097. 2014. View Article : Google Scholar : PubMed/NCBI
|
45
|
Wong QW, Li J, Ng SR, Lim SG, Yang H and
Vardy LA: RPL39L is an example of a recently evolved ribosomal
protein paralog that shows highly specific tissue expression
patterns and is upregulated in ESCs and HCC tumors. RNA Biol.
11:33–41. 2014. View Article : Google Scholar : PubMed/NCBI
|