|
1
|
Roseweir AK, McMillan DC, Horgan PG and
Edwards J: Colorectal cancer subtypes: Translation to routine
clinical pathology. Cancer Treat Rev. 57:1–7. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Punt CJ, Koopman M and Vermeulen L: From
tumour heterogeneity to advances in precision treatment of
colorectal cancer. Nat Rev Clin Oncol. 14:235–246. 2017. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Roychowdhury S and Chinnaiyan AM:
Translating cancer genomes and transcriptomes for precision
oncology. CA Cancer J Clin. 66:75–88. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Agesen TH, Sveen A, Merok MA, Lind GE,
Nesbakken A, Skotheim RI and Lothe RA: ColoGuideEx: A robust gene
classifier specific for stage II colorectal cancer prognosis. Gut.
61:1560–1567. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Hong Y, Downey T, Eu KW, Koh PK and Cheah
PY: A ‘metastasis-prone’ signature for early-stage mismatch-repair
proficient sporadic colorectal cancer patients and its implications
for possible therapeutics. Clin Exp Metastasis. 27:83–90. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Heijink DM, Fehrmann RS, de Vries EG,
Koornstra JJ, Oosterhuis D, van der Zee AG, Kleibeuker JH and de
Jong S: A bioinformatical and functional approach to identify novel
strategies for chemoprevention of colorectal cancer. Oncogene.
30:2026–2036. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Quan B, Qi X, Yu Z, Jiang Y, Liao M, Wang
G, Feng R, Zhang L, Chen Z, Jiang Q and Liu G: Pathway analysis of
genome-wide association study and transcriptome data highlights new
biological pathways in colorectal cancer. Mol Genet Genomics.
290:603–610. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
8
|
Wu Y, Wang X, Wu F, Huang R, Xue F, Liang
G, Tao M, Cai P and Huang Y: Transcriptome profiling of the cancer,
adjacent non-tumor and distant normal tissues from a colorectal
cancer patient by deep sequencing. PLoS One. 7:e410012012.
View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Kim ST, Sohn I, DO IG, Jang J, Kim SH,
Jung IH, Park JO, Park YS, Talasaz A, Lee J and Kim HC:
Transcriptome analysis of CD133-positive stem cells and prognostic
value of survivin in colorectal cancer. Cancer Genomics Proteomics.
11:259–266. 2014.PubMed/NCBI
|
|
10
|
Calon A, Espinet E, Palomo-Ponce S,
Tauriello DV, Iglesias M, Céspedes MV, Sevillano M, Nadal C, Jung
P, Zhang XH, et al: Dependency of colorectal cancer on a
TGF-beta-driven program in stromal cells for metastasis initiation.
Cancer Cell. 22:571–584. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Isella C, Terrasi A, Bellomo SE, Petti C,
Galatola G, Muratore A, Mellano A, Senetta R, Cassenti A, Sonetto
C, et al: Stromal contribution to the colorectal cancer
transcriptome. Nat Genet. 47:312–319. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Barrett T, Troup DB, Wilhite SE, Ledoux P,
Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH,
Sherman PM, et al: NCBI GEO: Archive for functional genomics data
sets-10 years on. Nucleic Acids Res. 39:D1005–1010. 2011.
View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Dai M, Wang P, Boyd AD, Kostov G, Athey B,
Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, et al: Evolving
gene/transcript definitions significantly alter the interpretation
of GeneChip data. Nucleic Acids Res. 33:e1752005. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Oldham MC, Konopka G, Iwamoto K,
Langfelder P, Kato T, Horvath S and Geschwind DH: Functional
organization of the transcriptome in human brain. Nat Neurosci.
11:1271–1282. 2008. View
Article : Google Scholar : PubMed/NCBI
|
|
15
|
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
|
|
16
|
Miller JA, Horvath S and Geschwind DH:
Divergence of human and mouse brain transcriptome highlights
Alzheimer disease pathways. Proc Natl Acad Sci USA.
107:12698–12703. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Langfelder P and Horvath S: WGCNA: An R
package for weighted correlation network analysis. BMC
Bioinformatics. 9:5592008. View Article : Google Scholar : PubMed/NCBI
|
|
18
|
da Huang W, 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
|
da Huang W, Sherman BT and Lempicki RA:
Bioinformatics enrichment tools: Paths toward the comprehensive
functional analysis of large gene lists. Nucleic Acids Res.
37:1–13. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Ashburner M, Ball CA, Blake JA, Botstein
D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT,
et al: Gene ontology: Tool for the unification of biology. The Gene
Ontology Consortium. Nat Genet. 25:25–29. 2000. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Smoot ME, Ono K, Ruscheinski J, Wang PL
and Ideker T: Cytoscape 2.8: New features for data integration and
network visualization. Bioinformatics. 27:431–432. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Liu R, Zhang W, Liu ZQ and Zhou HH:
Associating transcriptional modules with colon cancer survival
through weighted gene co-expression network analysis. BMC Genomics.
18:3612017. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Lanchbury J, Gutin A and Flake D: Cancer
prognosis signatures. Google Patents. 2016.
|
|
24
|
Scott RE, Ghule PN, Stein JL and Stein GS:
Cell cycle gene expression networks discovered using systems
biology: Significance in carcinogenesis. J Cell Physiol.
230:2533–2542. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Friedl P and Alexander S: Cancer invasion
and the microenvironment: Plasticity and reciprocity. Cell.
147:992–1009. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
26
|
Iijima J, Konno K and Itano N:
Inflammatory alterations of the extracellular matrix in the tumor
microenvironment. Cancers (Basel). 3:3189–3205. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Horvat M, Potocnik U, Repnik K, Kavalar R
and Stabuc B: Single nucleotide polymorphisms as prognostic and
predictive factors of adjuvant chemotherapy in colorectal cancer of
stages I and II. Gastroenterol Res Pract. 2016:21394892016.
View Article : Google Scholar : PubMed/NCBI
|
|
28
|
Conti J and Thomas G: The role of tumour
stroma in colorectal cancer invasion and metastasis. Cancers
(Basel). 3:2160–2168. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Edge SB and Compton CC: The American Joint
Committee on Cancer: The 7th edition of the AJCC cancer staging
manual and the future of TNM. Ann Surg Oncol. 17:1471–1474. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Ostman A and Augsten M: Cancer-associated
fibroblasts and tumor growth-bystanders turning into key players.
Curr Opin Genet Dev. 19:67–73. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Yoshihara K, Shahmoradgoli M, Martínez E,
Vegesna R, Kim H, Torres-Garcia W, Treviño V, Shen H, Laird PW,
Levine DA, et al: Inferring tumour purity and stromal and immune
cell admixture from expression data. Nat Commun. 4:26122013.
View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Tomita N, Jiang W, Hibshoosh H, Warburton
D, Kahn SM and Weinstein IB: Isolation and characterization of a
highly malignant variant of the SW480 human colon cancer cell line.
Cancer Res. 52:6840–6847. 1992.PubMed/NCBI
|
|
33
|
Park J and Scherer PE: Adipocyte-derived
endotrophin promotes malignant tumor progression. J Clin Invest.
122:4243–4256. 2012. View
Article : Google Scholar : PubMed/NCBI
|
|
34
|
Liu W, Li L and Li W: Gene co-expression
analysis identifies common modules related to prognosis and drug
resistance in cancer cell lines. Int J Cancer. 135:2795–2803. 2014.
View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Qiao J, Fang CY, Chen SX, Wang XQ, Cui SJ,
Liu XH, Jiang YH, Wang J, Zhang Y, Yang PY and Liu F: Stroma
derived COL6A3 is a potential prognosis marker of colorectal
carcinoma revealed by quantitative proteomics. Oncotarget.
6:29929–29946. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Yu J, Wu WK, Li X, He J, Li XX, Ng SS, Yu
C, Gao Z, Yang J, Li M, et al: Novel recurrently mutated genes and
a prognostic mutation signature in colorectal cancer. Gut.
64:636–645. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Joyce T, Cantarella D, Isella C, Medico E
and Pintzas A: A molecular signature for Epithelial to Mesenchymal
transition in a human colon cancer cell system is revealed by
large-scale microarray analysis. Clin Exp Metastasis. 26:569–587.
2009. View Article : Google Scholar : PubMed/NCBI
|
