Ferlay J, Autier P, Boniol M, Heanue M, Colombet M, Boyle P. Estimates of the cancer incidence and mortality in Europe in 2006. Ann Oncol. 2007;18(3):581.

Article
CAS
PubMed
Google Scholar

Siegel R, Ward E, Hao Y, Xu J, Murray T, Thun MJ. Cancer statistics, 2008. CA Cancer J Clin. 2008;58(2):71–96.

Article
PubMed
Google Scholar

Zhou JJ, Zheng S, Sun LF, Zheng L. MicroRNA regulation network in colorectal cancer metastasis. World J Biol Chem. 2014;5(3):301–7.

Article
PubMed
PubMed Central
Google Scholar

Sarver AL, French AJ, Borralho PM, Thayanithy V, Oberg AL, Silverstein KA, et al. Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states. BMC Cancer. 2009;9(1):401.

Article
PubMed
PubMed Central
Google Scholar

Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A. 2006;103(7):2257–61.

Article
CAS
PubMed
PubMed Central
Google Scholar

Slaby O, Svoboda M, Fabian P, Smerdova T, Knoflickova D, Bednarikova M, et al. Altered expression of miR-21, miR-31, miR-143 and miR-145 is related to clinicopathologic features of colorectal cancer. Oncology. 2007;72(5–6):397–402.

Article
CAS
PubMed
Google Scholar

Winter J, Jung S, Keller S, Gregory RI, Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol. 2009;11(3):228–34.

Article
CAS
PubMed
Google Scholar

Esquela-Kerscher A, Slack FJ. Oncomirs-microRNAs with a role in cancer. Nat Rev Cancer. 2006;6(4):259–69.

Article
CAS
PubMed
Google Scholar

Garzon R, Fabbri M, Cimmino A, Calin GA, Croce CM. MicroRNA expression and function in cancer. Trends Mol Med. 2006;12(12):580–7.

Article
CAS
PubMed
Google Scholar

Garzon R, Calin GA, Croce CM. MicroRNAs in cancer. Annu Rev Med. 2009;60:167–79.

Article
CAS
PubMed
Google Scholar

Michael MZ, O’Connor SM, van Holst Pellekaan NG, Young GP, James RJ. Reduced accumulation of specific MicroRNAs in colorectal neoplasia. Mol Cancer Res. 2003;1(12):882–91.

CAS
PubMed
Google Scholar

Croce CM, Calin GA. miRNAs, cancer, and stem cell division. Cell. 2005;122(1):6–7.

Article
CAS
PubMed
Google Scholar

Schetter AJ, Leung SY, Sohn JJ, Zanetti KA, Bowman ED, et al. MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. JAMA. 2008;299(4):425–36.

Article
CAS
PubMed
PubMed Central
Google Scholar

Schepeler T, Reinert JT, Ostenfeld MS, Christensen LL, Silahtaroglu AN, Dyrskjøt L, et al. Diagnostic and prognostic microRNAs in stage II colon cancer. Cancer Res. 2008;68(15):6416–24.

Article
CAS
PubMed
Google Scholar

Kalimutho M, Blanco GD, Di Cecilia S, Sileri P, Cretella M, Pallone F, et al. Differential expression of miR-144* as a novel fecal-based diagnostic marker for colorectal cancer. J Gastroenterol. 2011;46(12):1391–402.

Article
CAS
PubMed
Google Scholar

Huffaker TB, Hu R, Runtsch MC, Bake E, Chen X, Zhao J, et al. Epistasis between microRNAs 155 and 146a during T cell-mediated antitumor immunity. Cell Rep. 2012;2(6):1697–709.

Article
CAS
PubMed
PubMed Central
Google Scholar

Tibshirani R. Regression shrinkage and selection via the lasso**.** Journal of the Royal Statistical Society. Series B (Methodological). 1996;58(1):267–288.

Quitadamo A, Tian L, Hall B, Shi X. An integrated network of microRNA and gene expression in ovarian cancer. BMC Bioinformatics. 2015;16(5):S5. doi:10.1186/1471-2105-16-S5-S5.

Wang Z, Xu J, Shi X. Finding alternative expression quantitative trait loci by exploring sparse model space. J Comput Biol. 2014;21(5):385–93.

Article
CAS
PubMed
PubMed Central
Google Scholar

Tian L, Quitadamo A, Lin F, Shi X. Methods for population-based eQTL analysis in human genetics. Tsinghua Sci Technol. 2014;19(6):624–34.

Article
CAS
Google Scholar

Chen X, Shi X, Xu X, Wang Z, Mills R, Lee C, et al. A two-graph guided multi-task lasso approach for eQTL mapping. In: International Conference on Articial Intelligence and Statistics, vol. 12; 2012. p. 208–17.

Google Scholar

Cheng W, Shi Y, Zhang X, Wang W. Fast and robust group-wise eQTL mapping using sparse graphical models. BMC Bioinformatics. 2015;16(1):2.

Article
PubMed
PubMed Central
Google Scholar

Cheng W, Zhang X, Guo Z, Shi Y, Wang W. Graph-regularized dual Lasso for robust eQTL mapping. Bioinformatics. 2014;30(12):139–48.

Article
Google Scholar

Kim S, Xing EP. Tree-guided group lasso for multi-response regression with structured sparsity, with an application to eQTL mapping. Ann Appl Stat. 2012:1095–117.

Xu S. An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics. 2007;63(2):513–21.

Article
CAS
PubMed
Google Scholar

Huang Y, Wuchty S, Przytycka TM. eQTL epistasis challenges and computational approaches. Front Genet. 2013;4:51.

PubMed
PubMed Central
Google Scholar

Nelson MR, Kardia SL, Ferrell RE, Sing CF. A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res. 2001;11(3):458–70.

Article
CAS
PubMed
PubMed Central
Google Scholar

Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, et al. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet. 2001;69(1):138–47.

Article
CAS
PubMed
PubMed Central
Google Scholar

Kang M, Zhang C, Chun HW, Ding C, Liu C, Gao J. eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways. Bioinformatics. 2015;31(5):656–64.

Article
CAS
PubMed
Google Scholar

Xie M, Li J, Jiang T. Detecting genome-wide epistasis based on the clustering of relatively frequent items. Bioinformatics. 2012;28(1):5–12.

Article
CAS
PubMed
Google Scholar

Guo X, Zhang J, Cai Z, Du DZ, Pan Y. Searching genome-wide multi-locus associations for multiple diseases based on Bayesian Inference. IEEE/ACM Trans Comput Biol Bioinform. 2016;14(3):600–610.

Ding X, Wang J, Zelikovsky A, Guo X, Xie M, Pan Y. Searching high-order SNP combinations for complex diseases based on energy distribution difference. IEEE/ACM Trans Comput Biol Bioinform. 2015;12(3):695–704.

Article
CAS
PubMed
Google Scholar

Huang A, Xu S, Cai X. Empirical Bayesian elastic net for multiple quantitative trait locus mapping. Heredity. 2015;114(1):107–15.

Article
CAS
PubMed
Google Scholar

The Cancer Genome Atlas Project: The Cancer Genome Atlas (TCGA). https://tcga-data.nci.nih.gov/.

Cai X, Huang A, Xu S. Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping. BMC Bioinformatics. 2011;12(1):211.

Article
PubMed
PubMed Central
Google Scholar

Akao Y, Nakagawa Y, Naoe T. Let-7 microRNA functions as a potential growth suppressor in human colon cancer cells. Biol Pharm Bull. 2006;29(5):903–6.

Article
CAS
PubMed
Google Scholar

Bandrés E, Cubedo E, Agirre X, Malumbres R, Zarate R, Ramirez N, et al. Identification by real-time PCR of 13 mature microRNAs differentially expressed in colorectal cancer and non-tumoral tissues. Mol Cancer. 2006;5(1):29.

Article
PubMed
PubMed Central
Google Scholar

Olivier M, Hollstein M, Hainaut P. TP53 mutations in human cancers: origins, consequences, and clinical use. Cold Spring Harb Perspect Biol. 2010;2(1):a001008.

Article
PubMed
PubMed Central
Google Scholar

Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009;37(suppl 1):D98–104.

Article
CAS
PubMed
Google Scholar

Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005;120(1):15–20.

Article
CAS
PubMed
Google Scholar

Wong N, Wang X. miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 2015:43(D1):D146–D152.

Anastas JN, Moon RT. WNT signaling pathways as therapeutic targets in cancer. Nat Rev Cancer. 2013;13(1):11–26.

Article
CAS
PubMed
Google Scholar

Vishnubalaji R, Hamam R, Abdulla MH, Mohammed MA, Kassem M, Al-Obeed O, et al. Genome-wide mRNA and miRNA expression profiling reveal multiple regulatory networks in colorectal cancer. Cell Death Dis. 2015;6(1):e1614.

Article
CAS
PubMed
PubMed Central
Google Scholar

Meza-Sosa KF, Pérez-García EI, Camacho-Concha N, López-Gutiérrez O, Pedraza-Alva G, Pérez-Martínez L. MiR-7 promotes epithelial cell transformation by targeting the tumor suppressor KLF4. PLoS One. 2014;9(9):e103987.

Article
PubMed
PubMed Central
Google Scholar

Aherne ST, Madden SF, Hughes DJ, Pardini B, Naccarati A, Levy M, et al. Circulating miRNAs miR-34a and miR-150 associated with colorectal cancer progression. BMC Cancer. 2015;15(1):329.

Article
PubMed
PubMed Central
Google Scholar

Online Mendelian Inheritance in Man (OMIM). http://omim.org/. Accessed May 2016.

Samuels Y, Wang Z, Bardelli A, Silliman N, Ptak J, Szabo S, et al. High frequency of mutations of the PIK3CA gene in human cancers. Science. 2004;304(5670):554.

Article
CAS
PubMed
Google Scholar

Haigis KM, Kendall KR, Wang Y, Cheung A, Haigis MC, Glickman JN, et al. Differential effects of oncogenic K-Ras and N-Ras on proliferation, differentiation and tumor progression in the colon. Nat Genet. 2008;40(5):600–8.

Article
CAS
PubMed
PubMed Central
Google Scholar

Charames GS, Ramyar L, Mitri A, Berk T, Cheng H, Jung J, et al. A large novel deletion in the APC promoter region causes gene silencing and leads to classical familial adenomatous polyposis in a manitoba mennonite kindred. Hum Genet. 2008;124(5):535–41.

Article
CAS
PubMed
Google Scholar

Chisanga D, Keerthikumar S, Pathan M, Ariyaratne D, Kalra H, Boukouris S, et al. Colorectal cancer atlas: an integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues. Nucleic Acids Res. 2016;44(D1):D969–74.

Article
CAS
PubMed
Google Scholar

Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, et al. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009;25(2):288–9.

Article
CAS
PubMed
Google Scholar

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–9.

Article
CAS
PubMed
PubMed Central
Google Scholar

Gene Ontology Consortium. Gene ontology consortium: going forward. Nucleic Acids Res. 2015;43(D1):D1049–56.

Article
Google Scholar

Emmert-Streib F, de Matos Simoes R, Glazko G, McDade S, Haibe-Kains B, Holzinger A, et al. Functional and genetic analysis of the colon cancer network. BMC Bioinformatics. 2014, 15(6): Suppl 6.

Ettarh R, Cullen A, Calamai A. NSAIDs and cell proliferation in colorectal cancer. Pharmaceuticals. 2010;3(7):2007–21.

Article
CAS
PubMed
PubMed Central
Google Scholar

Li XL, Zhou J, Chen ZR, Chng WJ. P53 mutations in colorectal cancer-molecular pathogenesis and pharmacological reactivation. World J Gastroenterol. 2015;21(1):84–93.

Article
PubMed
PubMed Central
Google Scholar

Wang TY, Jia YL, Zhang X, Sun QL, Li YC, Zhang JH, et al. Treating colon cancer cells with FK228 reveals a link between histone lysine acetylation and extensive changes in the cellular proteome. Sci Rep. 2015;5

Li E, Ji P, Ouyang N, Zhang Y, Wang XY, Rubin DC, et al. Differential expression of miRNAs in colon cancer between African and Caucasian Americans: implications for cancer racial health disparities. Int J Oncol. 2014;45(2):587–94.

Article
PubMed
PubMed Central
Google Scholar

Arndt GM, Dossey L, Cullen LM, Lai A, Druker R, Eisbacher M, et al. Characterization of global microRNA expression reveals oncogenic potential of miR-145 in metastatic colorectal cancer. BMC Cancer. 2009;9(1):374.

Article
PubMed
PubMed Central
Google Scholar

Motoyama K, Inoue H, Takatsuno Y, Tanaka F, Mimori K, Uetake H, et al. Over-and under-expressed microRNAs in human colorectal cancer. Int J Oncol. 2009;34(4):1069.

CAS
PubMed
Google Scholar

Lee H, Flaherty P, Ji HP. Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis. BMC Med Genet. 2013;6(1):54.

Google Scholar

Nishida N, Nagahara M, Sato T, Mimori K, Sudo T, Tanaka F, et al. Microarray analysis of colorectal cancer stromal tissue reveals upregulation of two oncogenic miRNA clusters. Clin Cancer Res. 2012;18(11):3054–70.

Tazawa H, Tsuchiya N, Izumiya M, Nakagama H. Tumor-suppressive miR-34a induces senescence-like growth arrest through modulation of the E2F pathway in human colon cancer cells. Proc Natl Acad Sci. 2007;104(39):15472–7.

Article
CAS
PubMed
PubMed Central
Google Scholar