|
1
|
Siegel RL, Miller KD and Jemal A: Cancer
statistics, 2016. CA Cancer J Clin. 66:7–30. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Corley DA, Jensen CD, Marks AR, Zhao WK,
Lee JK, Doubeni CA, Zauber AG, de Boer J, Fireman BH, Schottinger
JE, et al: Adenoma detection rate and risk of colorectal cancer and
death. N Engl J Med. 370:1298–1306. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Sung JJ, Lau JY, Goh KL and Leung WK: Asia
Pacific Working Group on Colorectal Cancer: Increasing incidence of
colorectal cancer in Asia: Implications for screening. Lancet
Oncol. 6:871–876. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Radice E, Miranda V and Bellone G:
Low-doses of sequential-kinetic-activated interferon-γ enhance the
ex vivo cytotoxicity of peripheral blood natural killer cells from
patients with early-stage colorectal cancer. A preliminary study.
Int Immunopharmacol. 19:66–73. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Jo YK, Roh SA, Lee H, Park NY, Choi ES, Oh
JH, Park SJ, Shin JH, Suh YA, Lee EK, et al: Polypyrimidine
tract-binding protein 1-mediated down-regulation of ATG10
facilitates metastasis of colorectal cancer cells. Cancer Lett.
385:21–27. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Mullany LE, Herrick JS, Wolff RK and
Slattery ML: MicroRNA seed region length impact on target messenger
RNA expression and survival in colorectal cancer. PLoS One.
11:e01541772016. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Kan JY, Yen MC, Wang JY, Wu DC, Chiu YJ,
Ho YW and Kuo PL: Nesfatin-1/Nucleobindin-2 enhances cell
migration, invasion, and epithelial-mesenchymal transition via
LKB1/AMPK/TORC1/ZEB1 pathways in colon cancer. Oncotarget.
7:31336–31349. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
8
|
Unger C, Kramer N, Unterleuthner D,
Scherzer M, Burian A, Rudisch A, Stadler M, Schlederer M, Lenhardt
D, Riedl A, et al: Stromal-derived IGF2 promotes colon cancer
progression via paracrine and autocrine mechanisms. Oncogene.
36:5341–5355. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
McFadden EJ and Hargrove AE: Biochemical
methods to investigate lncRNA and the influence of lncRNA:protein
complexes on chromatin. Biochemistry. 55:1615–1630. 2016.
View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Liz J and Esteller M: lncRNAs and
microRNAs with a role in cancer development. Biochim Biophys Acta.
1859:169–176. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Lees-Miller SP, Beattie TL and Tainer JA:
Noncoding RNA joins Ku and DNA-PKcs for DNA-break resistance in
breast cancer. Nat Struct Mol Biol. 23:509–510. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Quinn JJ and Chang HY: Unique features of
long non-coding RNA biogenesis and function. Nat Rev Genet.
17:47–62. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
He X, Tan X, Wang X, Jin H, Liu L, Ma L,
Yu H and Fan Z: C-Myc-activated long noncoding RNA CCAT1 promotes
colon cancer cell proliferation and invasion. Tumour Biol.
35:12181–12188. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Yue B, Qiu S, Zhao S, Liu C, Zhang D, Yu
F, Peng Z and Yan D: LncRNA-ATB mediated E-cadherin repression
promotes the progression of colon cancer and predicts poor
prognosis. J Gastroenterol Hepatol. 31:595–603. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Thorenoor N, Faltejskova-Vychytilova P,
Hombach S, Mlcochova J, Kretz M, Svoboda M and Slaby O: Long
non-coding RNA ZFAS1 interacts with CDK1 and is involved in
p53-dependent cell cycle control and apoptosis in colorectal
cancer. Oncotarget. 7:622–637. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Harrow J, Frankish A, Gonzalez JM,
Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa
A, Searle S, et al: GENCODE: The reference human genome annotation
for The ENCODE Project. Genome Res. 22:1760–1774. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Soneson C and Delorenzi M: A comparison of
methods for differential expression analysis of RNA-seq data. BMC
Bioinformatics. 14:912013. View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Robinson MD, McCarthy DJ and Smyth GK:
edgeR: A Bioconductor package for differential expression analysis
of digital gene expression data. Bioinformatics. 26:139–140. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
19
|
Law CW, Chen Y, Shi W and Smyth GK: voom:
Precision weights unlock linear model analysis tools for RNA-seq
read counts. Genome Biol. 15:R292014. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW,
Shi W and Smyth GK: limma powers differential expression
analyses for RNA-sequencing and microarray studies. Nucleic Acids
Res. 43:e472015. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Benjamini Y and Hochberg Y: Controlling
the false discovery rate: A practical and powerful approach to
multiple testing. J R Stat Soc B. 57:289–300. 1995.
|
|
22
|
Huang DW, Sherman BT, Tan Q, Kir J, Liu D,
Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, et al: DAVID
Bioinformatics Resources: Expanded annotation database and novel
algorithms to better extract biology from large gene lists. Nucleic
Acids Res. 35 Suppl 2:W169–175. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Ashburner M, Ball CA, Blake JA, Botstein
D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT,
et al: The Gene Ontology Consortium: Gene ontology: Tool for the
unification of biology. Nat Genet. 25:25–29. 2000. View Article : Google Scholar : PubMed/NCBI
|
|
24
|
Kanehisa M, Goto S, Kawashima S, Okuno Y
and Hattori M: The KEGG resource for deciphering the genome.
Nucleic Acids Res. 32:D277–D280. 2004. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Chatr-Aryamontri A, Breitkreutz BJ,
Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A,
Kolas N, O'Donnell L, et al: The BioGRID interaction database: 2015
update. Nucleic Acids Res. 43:D470–D478. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
26
|
Kohl M, Wiese S and Warscheid B:
Cytoscape: Software for visualization and analysis of biological
networks. Methods Mol Biol. 291–303. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Tang Y, Li M, Wang J, Pan Y and Wu FX:
CytoNCA: A cytoscape plugin for centrality analysis and evaluation
of protein interaction networks. Biosystems. 127:67–72. 2015.
View Article : Google Scholar : PubMed/NCBI
|
|
28
|
He X and Zhang J: Why do hubs tend to be
essential in protein networks? PLoS Genet. 2:e882006. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Bader GD and Hogue CW: An automated method
for finding molecular complexes in large protein interaction
networks. BMC Bioinformatics. 4:22003. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Yu G, Wang L-G, Han Y and He Q-Y:
clusterProfiler: An R package for comparing biological themes among
gene clusters. OMICS. 16:284–287. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Xie J and Liu C: Adjusted Kaplan-Meier
estimator and log-rank test with inverse probability of treatment
weighting for survival data. Stat Med. 24:3089–3110. 2005.
View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Ishwaran H, Kogalur UB, Blackstone EH and
Lauer MS: Random survival forests. Ann Appl Stat. 2:841–860. 2008.
View Article : Google Scholar
|
|
33
|
Ishwaran H: Variable importance in binary
regression trees and forests. Electron J Stat. 1:519–537. 2007.
View Article : Google Scholar
|
|
34
|
Villanueva A, Portela A, Sayols S,
Battiston C, Hoshida Y, Méndez-González J, Imbeaud S, Letouzé E,
Hernandez-Gea V, Cornella H, et al: HEPTROMIC Consortium: DNA
methylation-based prognosis and epidrivers in hepatocellular
carcinoma. Hepatology. 61:1945–1956. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Berkes CA and Tapscott SJ: MyoD and the
transcriptional control of myogenesis. Semin Cell Dev Biol.
16:585–595. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Kusano S and Raab-Traub N: I-mfa domain
proteins interact with Axin and affect its regulation of the Wnt
and c-Jun N-terminal kinase signaling pathways. Mol Cell Biol.
22:6393–6405. 2002. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Amado NG, Predes D, Fonseca BF, Cerqueira
DM, Reis AH, Dudenhoeffer AC, Borges HL, Mendes FA and Abreu JG:
Isoquercitrin suppresses colon cancer cell growth in vitro by
targeting the Wnt/β-catenin signaling pathway. J Biol Chem.
289:35456–35467. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Li J, Chen C, Bi X, Zhou C, Huang T, Ni C,
Yang P, Chen S, Ye M and Duan S: DNA methylation of CMTM3,
SSTR2, and MDFI genes in colorectal cancer. Gene.
630:1–7. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
39
|
Chen Y, Rabson AB and Gorski DH: MEOX2
regulates nuclear factor-kappaB activity in vascular endothelial
cells through interactions with p65 and IkappaBbeta. Cardiovasc
Res. 87:723–731. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Stegemann JP, Hong H and Nerem RM:
Mechanical, biochemical, and extracellular matrix effects on
vascular smooth muscle cell phenotype. J Appl Physiol 1985.
98:2321–2327. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Herbert SP and Stainier DY: Molecular
control of endothelial cell behaviour during blood vessel
morphogenesis. Nat Rev Mol Cell Biol. 12:551–564. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
42
|
Baeten CI, Hillen F, Pauwels P, de Bruine
AP and Baeten CG: Prognostic role of vasculogenic mimicry in
colorectal cancer. Dis Colon Rectum. 52:2028–2035. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
43
|
Babykutty S, Suboj P, Srinivas P, Nair AS,
Chandramohan K and Gopala S: Insidious role of nitric oxide in
migration/invasion of colon cancer cells by upregulating MMP-2/9
via activation of cGMP-PKG-ERK signaling pathways. Clin Exp
Metastasis. 29:471–492. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Li N, Xi Y, Tinsley HN, Gurpinar E, Gary
BD, Zhu B, Li Y, Chen X, Keeton AB, Abadi AH, et al: Sulindac
selectively inhibits colon tumor cell growth by activating the
cGMP/PKG pathway to suppress Wnt/β-catenin signaling. Mol Cancer
Ther. 12:1848–1859. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
45
|
Raveh E, Matouk IJ, Gilon M and Hochberg
A: The H19 Long non-coding RNA in cancer initiation, progression
and metastasis - a proposed unifying theory. Mol Cancer.
14:1842015. View Article : Google Scholar : PubMed/NCBI
|
|
46
|
Iguchi T, Uchi R, Nambara S, Saito T,
Komatsu H, Hirata H, Ueda M, Sakimura S, Takano Y, Kurashige J, et
al: A long noncoding RNA, lncRNA-ATB, is involved in the
progression and prognosis of colorectal cancer. Anticancer Res.
35:1385–1388. 2015.PubMed/NCBI
|
|
47
|
Xu TP, Huang MD, Xia R, Liu XX, Sun M, Yin
L, Chen WM, Han L, Zhang EB, Kong R, et al: Decreased expression of
the long non-coding RNA FENDRR is associated with poor
prognosis in gastric cancer and FENDRR regulates gastric
cancer cell metastasis by affecting fibronectin1 expression. J
Hematol Oncol. 7:632014. View Article : Google Scholar : PubMed/NCBI
|
|
48
|
Zhou M, Sun Y, Sun Y, Xu W, Zhang Z, Zhao
H, Zhong Z and Sun J: Comprehensive analysis of lncRNA expression
profiles reveals a novel lncRNA signature to discriminate
nonequivalent outcomes in patients with ovarian cancer. Oncotarget.
7:32433–32448. 2016.PubMed/NCBI
|
|
49
|
Sun J, Chen X, Wang Z, Guo M, Shi H, Wang
X, Cheng L and Zhou M: A potential prognostic long non-coding RNA
signature to predict metastasis-free survival of breast cancer
patients. Sci Rep. 5:165532015. View Article : Google Scholar : PubMed/NCBI
|
|
50
|
Li J, Chen Z, Tian L, Zhou C, He MY, Gao
Y, Wang S, Zhou F, Shi S, Feng X, et al: LncRNA profile study
reveals a three-lncRNA signature associated with the survival of
patients with oesophageal squamous cell carcinoma. Gut.
63:1700–1710. 2014. View Article : Google Scholar : PubMed/NCBI
|
|
51
|
Li Q, Dai Y, Wang F and Hou S:
Differentially expressed long non-coding RNAs and the prognostic
potential in colorectal cancer. Neoplasma. 63:977–983. 2016.
View Article : Google Scholar : PubMed/NCBI
|
|
52
|
Lian Y, Yan C, Ding J, Xia R, Ma Z, Hui B,
Ji H, Zhou J and Wang K: A novel lncRNA, LL22NC03-N64E9.1,
represses KLF2 transcription through binding with EZH2 in
colorectal cancer. Oncotarget. 8:59435–59445. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
53
|
Sakurai K, Reon BJ, Anaya J and Dutta A:
The lncRNA DRAIC/PCAT29 locus constitutes a
tumor-suppressive nexus. Mol Cancer Res. 13:828–838. 2015.
View Article : Google Scholar : PubMed/NCBI
|
