Abstract
Cancer is a multifactorial disease caused by the malfunction and modification of numerous biological entities, including genes, proteins, mRNAs, miRNAs, and metabolites. Recent advances in high-throughput technologies have generated massive amounts of diverse biological data, allowing researchers to investigate a large number of omics markers. While analyzing single omics data sets can reveal a wealth of information in a unidirectional fashion, because DNA, RNA, protein, and metabolite frequently collaborate to perform biological functions, the complementary effects and interactions between multiple molecular layers cannot be fully assessed. As a result, only by integrating multiple types of omics data can we gain a systematic and comprehensive understanding of the functional mechanisms underlying DNA-level alterations in tumors and identify novel genes, markers, vital networks, and pathways. We will briefly discuss the current state of colorectal cancer, liver cancer, and lung cancer research in this article. Additionally, we discuss various multi-omics analyses conducted in the fields of colorectal cancer, liver cancer, and lung cancer research, which provide insight into novel cancer diagnostic and treatment approaches. We hope to inspire researchers to use multi-omics approaches to investigate cancer at the molecular, cellular, and systemic levels.
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Aarons CB, Shanmugan S, Bleier JI. Management of malignant colon polyps: current status and controversies. World J Gastroenterol. 2014;20:16178–83.
Ahmed Z. Practicing precision medicine with intelligently integrative clinical and multi-omics data analysis. Hum Genomics. 2020;14:35.
Alberg AJ, Brock MV, Samet JM. Epidemiology of lung cancer: looking to the future. J Clin Oncol. 2005;23:3175–85.
Alberg AJ, Samet JM. Epidemiology of lung cancer. Chest. 2003;123:21S–49S.
Almusawi S, Ahmed M, Nateri AS. Understanding cell-cell communication and signaling in the colorectal cancer microenvironment. Clin Transl Med. 2021;11:e308.
Altenbuchinger M, Weihs A, Quackenbush J, Grabe HJ, Zacharias HU. Gaussian and mixed graphical models as (multi-)omics data analysis tools. Biochim Biophys Acta Gene Regul Mech. 2020;1863:194418.
Antoine M, Vieira T, Fallet V, Hamard C, Duruisseaux M, Cadranel J, Wislez M. Pulmonary sarcomatoid carcinoma. Ann Pathol. 2016;36:44–54.
Ariff B, Lloyd CR, Khan S, Shariff M, Thillainayagam AV, Bansi DS, Khan SA, Taylor-Robinson SD, Lim AKP. Imaging of liver cancer. World J Gastroenterol. 2009;15:1289–300.
Arora M, Kumari S, Singh J, Chopra A, Chauhan SS. PAXX, not NHEJ1 is an independent prognosticator in colon cancer. Front Mol Biosci. 2020;7:584053.
Asada K, Kobayashi K, Joutard S, Tubaki M, Takahashi S, Takasawa K, Komatsu M, Kaneko S, Sese J, Hamamoto R. Uncovering prognosis-related genes and pathways by multi-omics analysis in lung cancer. Biomol Ther. 2020;10
Ayiomamitis GD, Notas G, Vasilakaki T, Tsavari A, Vederaki S, Theodosopoulos T, Kouroumalis E, Zaravinos A. Understanding the interplay between COX-2 and hTERT in colorectal cancer using a multi-omics analysis. Cancers (Basel). 2019;11:1536.
Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehar J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jane-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P Jr, De Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, Macconaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. The cancer cell line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483:603–7.
Barta JA, Powell CA, Wisnivesky JP. Global epidemiology of lung cancer. Ann Glob Health. 2019;85:8.
Behjati S, Tarpey PS. What is next generation sequencing? Arch Dis Child Educ Pract Ed. 2013;98:236–8.
Berg KCG, Eide PW, Eilertsen IA, Johannessen B, Bruun J, Danielsen SA, Bjornslett M, Meza-Zepeda LA, Eknaes M, Lind GE, Myklebost O, Skotheim RI, Sveen A, Lothe RA. Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies. Mol Cancer. 2017;16:116.
Bishayee A "The Role of Inflammation in Liver Cancer," in Inflammation and Cancer, eds. B.B. Aggarwal, B. Sung & S.C. Gupta.), 2014 401–435.
Biswas N, Chakrabarti S. Artificial intelligence (AI)-based systems biology approaches in multi-omics data analysis of cancer. Front Oncol. 2020;10:588221.
Bosch FX, Ribes J, Borras J. Epidemiology of primary liver cancer. Semin Liver Dis. 1999;19:271–85.
Bosch FX, Ribes J, Diaz M, Cleries R. Primary liver cancer: worldwide incidence and trends. Gastroenterology. 2004;127:S5–S16.
Canzler S, Schor J, Busch W, Schubert K, Rolle-Kampczyk UE, Seitz H, Kamp H, Von Bergen M, Buesen R, Hackermuller J. Prospects and challenges of multi-omics data integration in toxicology. Arch Toxicol. 2020;94:371–88.
Center MM, Jemal A, Smith RA, Ward E. Worldwide variations in colorectal. Cancer. 2009;59:366–78.
Chakraborty S, Hosen MI, Ahmed M, Shekhar HU. Onco-multi-OMICS approach: a new frontier in cancer research. Biomed Res Int. 2018;2018:9836256.
Chang MH. Prevention of hepatitis B virus infection and liver cancer. Recent Results Cancer Res. 2014;193:75–95.
Chaudhary K, Poirion OB, Lu L, Garmire LX. Deep learning-based multi-omics integration robustly predicts survival in liver cancer. Clin Cancer Res. 2018;24:1248–59.
Chauvel C, Novoloaca A, Veyre P, Reynier F, Becker J. Evaluation of integrative clustering methods for the analysis of multi-omics data. Brief Bioinform. 2020;21:541–52.
Chen JG, Zhang SW. Liver cancer epidemic in China: past, present and future. Semin Cancer Biol. 2011;21:59–69.
Chen Z, Fillmore CM, Hammerman PS, Kim CF, Wong KK. Non-small-cell lung cancers: a heterogeneous set of diseases. Nat Rev Cancer. 2014;14:535–46.
Cheng WC, Chung IF, Chen CY, Sun HJ, Fen JJ, Tang WC, Chang TY, Wong TT, Wang HW. DriverDB: an exome sequencing database for cancer driver gene identification. Nucleic Acids Res. 2014;42:D1048-1054.
Chung IF, Chen CY, Su SC, Li CY, Wu KJ, Wang HW, Cheng WC. DriverDBv2: a database for human cancer driver gene research. Nucleic Acids Res. 2016;44:D975-979.
Chyr J, Zhang Z, Chen X, Zhou X. PredTAD: a machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines. Comput Struct Biotechnol J. 2021;19:2870–80.
Cieslik M, Chinnaiyan AM. Global genomics project unravels cancer's complexity at unprecedented scale. Nature. 2020;578:39–40.
Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot TS, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G, Noushmehr H. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res. 2016;44:e71.
Das T, Andrieux G, Ahmed M, Chakraborty S. Integration of online omics-data resources for cancer research. Front Genet. 2020;11:578345.
De Groot PM, Wu CC, Carter BW, Munden RF. The epidemiology of lung cancer. Transl Lung Cancer Res. 2018;7:220–33.
De Sousa VML, Carvalho L. Heterogeneity in lung cancer. Pathobiology. 2018;85:96–107.
Dienstmann R, Vermeulen L, Guinney J, Kopetz S, Tejpar S, Tabernero J. Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer. Nat Rev Cancer. 2017;17:79–92.
Dimitrakopoulos C, Hindupur SK, Colombi M, Liko D, Ng CKY, Piscuoglio S, Behr J, Moore AL, Singer J, Ruscheweyh HJ, Matter MS, Mossmann D, Terracciano LM, Hall MN, Beerenwinkel N. Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma. BMC Genomics. 2021;22:592.
Domon B, Aebersold R. Mass spectrometry and protein analysis. Science. 2006;312:212–7.
Du W, Elemento O. Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies. Oncogene. 2015;34:3215–25.
Eicher T, Kinnebrew G, Patt A, Spencer K, Ying K, Ma Q, Machiraju R, Mathe AEA. Metabolomics and multi-omics integration: a survey of computational methods and resources. Meta. 2020;10:202.
Fearon ER. "Molecular genetics of colorectal cancer," in Cancer prevention: from the laboratory to the clinic: implications of genetic, molecular, and preventive research, eds. H.L. Bradlow, M.P. Osborne & U. Veronesi.), 1995 101–110.
Gao Q, Zhu HW, Dong LQ, Shi WW, Chen R, Song ZJ, Huang C, Li JQ, Dong XW, Zhou YT, Liu Q, Ma LJ, Wang XY, Zhou J, Liu YS, Boja E, Robles AI, Ma WP, Wang P, Li YZ, Ding L, Wen B, Zhang B, Rodriguez H, Gao DM, Zhou H, Fan J. Integrated proteogenomic characterization of HBV-related hepatocellular carcinoma. Cell. 2019;179:561.
Ghaffari S, Hanson C, Schmidt RE, Bouchonville KJ, Offer SM, Sinha S. An integrated multi-omics approach to identify regulatory mechanisms in cancer metastatic processes. Genome Biol. 2021;22:19.
Ghosh D, Bernstein JA, Khurana Hershey GK, Rothenberg ME, Mersha TB. Leveraging multilayered "omics" data for atopic dermatitis: a road map to precision medicine. Front Immunol. 2018;9:2727.
Graw S, Chappell K, Washam CL, Gies A, Bird J, Robeson MS 2nd, Byrum SD. Multi-omics data integration considerations and study design for biological systems and disease. Mol Omics. 2021;17:170–85.
Hao Y, Li D, Xu Y, Ouyang J, Wang Y, Zhang Y, Li B, Xie L, Qin G. Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data. BMC Bioinformatics. 2019;20:195.
Hausman DM. What is cancer? Perspect Biol Med. 2019;62:778–84.
Herbst RS, Morgensztern D, Boshoff C. The biology and management of non-small cell lung cancer. Nature. 2018;553:446–54.
Holowatyj AN, Haffa M, Lin T, Scherer D, Gigic B, Ose J, Warby CA, Himbert C, Abbenhardt-Martin C, Achaintre D, Boehm J, Boucher KM, Gicquiau A, Gsur A, Habermann N, Herpel E, Kauczor HU, Keski-Rahkonen P, Kloor M, Von Knebel-Doeberitz M, Kok DE, Nattenmuller J, Schirmacher P, Schneider M, Schrotz-King P, Simon T, Ueland PM, Viskochil R, Weijenberg MP, Scalbert A, Ulrich A, Bowers LW, Hursting SD, Ulrich CM. Multi-omics analysis reveals adipose-tumor crosstalk in patients with colorectal cancer. Cancer Prev Res (Phila). 2020;13:817–28.
Hu W, Yang Y, Li X, Huang M, Xu F, Ge W, Zhang S, Zheng S. Multi-omics approach reveals distinct differences in left- and right-sided colon cancer. Mol Cancer Res. 2018;16:476–85.
Hu Z, Bi G, Sui Q, Bian Y, Du Y, Liang J, Li M, Zhan C, Lin Z, Wang Q. Analyses of multi-omics differences between patients with high and low PD1/PDL1 expression in lung squamous cell carcinoma. Int Immunopharmacol. 2020;88:106910.
Huang L, Brunell D, Stephan C, Mancuso J, Yu X, He B, Thompson TC, Zinner R, Kim J, Davies P, Wong STC. Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction. Bioinformatics. 2019;35:3709–17.
Huang S, Chaudhary K, Garmire LX. More is better: recent progress in multi-omics data integration methods. Front Genet. 2017;8:84.
Huang Y, Duanmu J, Liu Y, Yan M, Li T, Jiang Q. Analysis of multi-omics differences in left-side and right-side colon cancer. PeerJ. 2021;9:e11433.
Jahanafrooz Z, Mosafer J, Akbari M, Hashemzaei M, Mokhtarzadeh A, Baradaran B. Colon cancer therapy by focusing on colon cancer stem cells and their tumor microenvironment. J Cell Physiol. 2020;235:4153–66.
Jones GS, Baldwin DR. Recent advances in the management of lung cancer. Clin Med (Lond). 2018;18:s41–6.
Kel AE, Stegmaier P, Valeev T, Koschmann J, Poroikov V, Kel-Margoulis OV, Wingender E. Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. EuPA Open Proteom. 2016;13:1–13.
Kim TH, Dekker J. ChIP-seq. Cold Spring Harb Protoc; 2018.
Koch A, De Meyer T, Jeschke J, Van Criekinge W. MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data. BMC Genomics. 2015;16:636.
Koch A, Jeschke J, Van Criekinge W, Van Engeland M, De Meyer T. MEXPRESS update 2019. Nucleic Acids Res. 2019;47:W561–5.
Kong Y, Qiao Z, Ren Y, Genchev GZ, Ge M, Xiao H, Zhao H, Lu H. Integrative analysis of membrane proteome and MicroRNA reveals novel lung cancer metastasis biomarkers. Front Genet. 2020;11:1023.
Lam K, Pan K, Linnekamp JF, Medema JP, Kandimalla R. DNA methylation based biomarkers in colorectal cancer: a systematic review. Biochim Biophys Acta. 2016;1866:106–20.
Lee TY, Huang KY, Chuang CH, Lee CY, Chang TH. Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication. Comput Biol Chem. 2020;87:107277.
Li L, Wang H. Heterogeneity of liver cancer and personalized therapy. Cancer Lett. 2016;379:191–7.
Li P, Guo M, Sun B. Integration of multi-omics data to mine cancer-related gene modules. J Bioinforma Comput Biol. 2019;17:1950038.
Lin S, Yin YA, Jiang X, Sahni N, Yi S. Multi-OMICs and genome editing perspectives on liver cancer signaling networks. Biomed Res Int. 2016;2016:6186281.
Liu CY, Chen KF, Chen PJ. Treatment of liver cancer. Cold Spring Harb Perspect Med. 2015;5:a021535.
Liu SH, Shen PC, Chen CY, Hsu AN, Cho YC, Lai YL, Chen FH, Li CY, Wang SC, Chen M, Chung IF, Cheng WC. DriverDBv3: a multi-omics database for cancer driver gene research. Nucleic Acids Res. 2020a;48:D863–70.
Liu X, Qin J, Gao T, Li C, Chen X, Zeng K, Xu M, He B, Pan B, Xu X, Pan Y, Sun H, Xu T, Wang S. Analysis of METTL3 and METTL14 in hepatocellular carcinoma. Aging (Albany NY). 2020b;12:21638–59.
Liu XN, Cui DN, Li YF, Liu YH, Liu G, Liu L. Multiple "omics" data-based biomarker screening for hepatocellular carcinoma diagnosis. World J Gastroenterol. 2019;25:4199–212.
Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, Meyerson M, Zhang X. Multi-omics analysis identifies MGA as a negative regulator of the MYC pathway in lung adenocarcinoma. Mol Cancer Res. 2020;18:574–84.
Lu Y, Li Q, Zheng K, Fu C, Jiang C, Zhou D, Xia C, Ma S. Development of a high efficient promoter finding method based on transient transfection. Gene X. 2019;2:100008.
Luan M, Song F, Qu S, Meng X, Ji J, Duan Y, Sun C, Si H, Zhai H. Multi-omics integrative analysis and survival risk model construction of non-small cell lung cancer based on The Cancer Genome Atlas datasets. Oncol Lett. 2020;20:58.
Lv J, Wang J, Shang X, Liu F, Guo S. Survival prediction in patients with colon adenocarcinoma via multi-omics data integration using a deep learning algorithm. Biosci Rep. 2020;40:BSR20201482.
Mantini G, Pham TV, Piersma SR, Jimenez CR. Computational analysis of Phosphoproteomics data in multi-omics cancer studies. Proteomics. 2021;21:e1900312.
Marengo A, Rosso C, Bugianesi E. Liver cancer: connections with obesity, fatty liver, and cirrhosis. Annu Rev Med. 2016;67:103–17.
Mármol I, Sánchez-De-Diego C, Pradilla Dieste A, Cerrada E, Rodriguez Yoldi MJ. Colorectal carcinoma: a general overview and future perspectives in colorectal cancer. Int J Mol Sci. 2017;18:197.
Matthiesen R, Jensen ON. Analysis of mass spectrometry data in proteomics. Methods Mol Biol. 2008;453:105–22.
Mcglynn KA, Tsao L, Hsing AW, Devesa SS, Fraumeni JF. International trends and patterns of primary liver cancer. Int J Cancer. 2001;94:290–6.
Mckillop IH, Schrum LW. Alcohol and liver cancer. Alcohol. 2005;35:195–203.
Meng C, Zeleznik OA, Thallinger GG, Kuster B, Gholami AM, Culhane AC. Dimension reduction techniques for the integrative analysis of multi-omics data. Brief Bioinform. 2016;17:628–41.
Miao R, Luo H, Zhou H, Li G, Bu D, Yang X, Zhao X, Zhang H, Liu S, Zhong Y, Zou Z, Zhao Y, Yu K, He L, Sang X, Zhong S, Huang J, Wu Y, Miksad RA, Robson SC, Jiang C, Zhao Y, Zhao H. Identification of prognostic biomarkers in hepatitis B virus-related hepatocellular carcinoma and stratification by integrative multi-omics analysis. J Hepatol. 2014;61:840–9.
Minna JD, Roth JA, Gazdar AF. Focus on lung cancer. Cancer Cell. 2002;1:49–52.
Nakano D, Kawaguchi T, Iwamoto H, Hayakawa M, Koga H, Torimura T. Effects of canagliflozin on growth and metabolic reprograming in hepatocellular carcinoma cells: multi-omics analysis of metabolomics and absolute quantification proteomics (iMPAQT). PLoS One. 2020;15:e0232283.
Netanely D, Stern N, Laufer I, Shamir R. PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. BMC Bioinformatics. 2019;20:732.
Nicora G, Vitali F, Dagliati A, Geifman N, Bellazzi R. Integrated multi-omics analyses in oncology: a review of machine learning methods and tools. Front Oncol. 2020;10:1030.
Nusinow DP, Szpyt J, Ghandi M, Rose CM, Mcdonald ER 3rd, Kalocsay M, Jane-Valbuena J, Gelfand E, Schweppe DK, Jedrychowski M, Golji J, Porter DA, Rejtar T, Wang YK, Kryukov GV, Stegmeier F, Erickson BK, Garraway LA, Sellers WR, Gygi SP. Quantitative proteomics of the cancer cell line Encyclopedia. Cell. 2020;180(387–402):e316.
O'connell JB, Maggard MA, Livingston EH, Yo CK. Colorectal cancer in the young. Am J Surg. 2004;187:343–8.
Ouyang X, Fan Q, Ling G, Shi Y, Hu F. Identification of diagnostic biomarkers and subtypes of liver hepatocellular carcinoma by multi-omics data analysis. Genes (Basel). 2020;11:1051.
Park M, Kim D, Moon K, Park T. Integrative analysis of multi-omics data based on blockwise sparse principal components. Int J Mol Sci. 2020;21:8202.
Pastushenko I, Blanpain C. EMT transition states during tumor progression and metastasis. Trends Cell Biol. 2019;29:212–26.
Patz EF, Goodman PC, Bepler G. Current concepts—screening for lung cancer. N Engl J Med. 2000;343:1627–33.
Potter JD. Colorectal cancer: molecules and populations. J Natl Cancer Inst. 1999;91:916–32.
Preisser F, Cooperberg MR, Crook J, Feng F, Graefen M, Karakiewicz PI, Klotz L, Montironi R, Nguyen PL, D'amico AV. Intermediate-risk prostate cancer: stratification and management. Eur Urol Oncol. 2020;3:270–80.
Rhee EP. How omics data can be used in nephrology. Am J Kidney Dis. 2018;72:129–35.
Salgia R, Skarin AT. Molecular abnormalities in lung cancer. J Clin Oncol. 1998;16:1207–17.
Shen H, Yang J, Huang Q, Jiang MJ, Tan YN, Fu JF, Zhu LZ, Fang XF, Yuan Y. Different treatment strategies and molecular features between right-sided and left-sided colon cancers. World J Gastroenterol. 2015;21:6470–8.
Shen M, Xu M, Zhong F, Crist MC, Prior AB, Yang K, Allaire DM, Choueiry F, Zhu J, Shi H. A multi-omics study revealing the metabolic effects of Estrogen in liver cancer cells HepG2. Cell. 2021a;10:455.
Shen Y, Xiong W, Gu Q, Zhang Q, Yue J, Liu C, Wang D. Multi-omics integrative analysis uncovers molecular subtypes and mRNAs as therapeutic targets for liver cancer. Front Med (Lausanne). 2021b;8:654635.
Sia D, Villanueva A, Friedman SL, Llovet JM. Liver cancer cell of origin, molecular class, and effects on patient prognosis. Gastroenterology. 2017;152:745–61.
Siegel R, Desantis C, Jemal A. Colorectal cancer statistics, 2014. CA-a Cancer J Clin. 2014;64:104–17.
Song J, Yang J, Lin R, Cai X, Zheng L, Chen Y. Molecular heterogeneity of guanine nucleotide binding-protein gamma subunit 4 in left- and right-sided colon cancer. Oncol Lett. 2020;20:334.
Spiro SG, Silvestri GA. One hundred years of lung cancer. Am J Respir Crit Care Med. 2005;172:523–9.
Srivatanakul P, Sriplung H, Deerasamee S. Epidemiology of liver cancer: an overview. Asian Pac J Cancer Prev. 2004;5:118–25.
Stintzing S. Management of colorectal cancer. F1000Prime Rep. 2014;6:108.
Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics data integration, interpretation, and its application. Bioinform Biol Insights. 2020;14:1–24.
Sun YV, Hu YJ. Integrative analysis of multi-omics data for discovery and functional studies of complex human diseases. Adv Genet. 2016;93:147–90.
Sung H, Ferlay J, Siegel RL, Laversanne M, and Bray, F.J.C.a.C.J.F.C.. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. 2021, 71.
Tomczak K, Czerwinska P, Wiznerowicz M. The cancer genome atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Pozn). 2015;19:A68-77.
Tong D, Tian Y, Zhou T, Ye Q, Li J, Ding K, Li J. Improving prediction performance of colon cancer prognosis based on the integration of clinical and multi-omics data. BMC Med Inform Decis Mak. 2020;20:22.
Torre LA, Siegel RL, Jemal A. Lung cancer statistics. Adv Exp Med Biol. 2016a;893:1–19.
Torre LA, Siegel RL, Ward EM, Jemal A. Global cancer incidence and mortality rates and trends-an update. Cancer Epidemiol Biomark Prev. 2016b;25:16–27.
Valencia AM, Kadoch C. Chromatin regulatory mechanisms and therapeutic opportunities in cancer. Nat Cell Biol. 2019;21:152–61.
Van Meerbeeck JP, Fennell DA, De Ruysscher DKM. Small-cell lung cancer. Lancet. 2011;378:1741–55.
Vasaikar SV, Straub P, Wang J, Zhang B. LinkedOmics: analyzing multi-omics data within and across 32 cancer types. Nucleic Acids Res. 2018;46:D956–63.
Wang C, Yang F, Chen T, Dong Q, Zhao Z, Liu Y, Chen B, Liang H, Yang H, Gu Y. RHPCG: a database of the regulation of the hippo pathway in cancer genome. Database (Oxford). 2019;2019:baz135.
Wang Z, Jensen MA, Zenklusen JC. A practical guide to the cancer genome atlas (TCGA). Methods Mol Biol. 2016;1418:111–41.
Wang Z, Wei Y, Zhang R, Su L, Gogarten SM, Liu G, Brennan P, Field JK, Mckay JD, Lissowska J, Swiatkowska B, Janout V, Bolca C, Kontic M, Scelo G, Zaridze D, Laurie CC, Doheny KF, Pugh EK, Marosy BA, Hetrick KN, Xiao X, Pikielny C, Hung RJ, Amos CI, Lin X, Christiani DC. Multi-omics analysis reveals a HIF network and hub gene EPAS1 associated with lung adenocarcinoma. EBioMedicine. 2018;32:93–101.
Weinberg DS, Schoen RE. Screening for colorectal cancer. Ann Intern Med. 2014;160
Weinberg RA. How cancer arises. Sci Am. 1996;275:62–70.
Wistuba I, Gazdar AF. Lung cancer preneoplasia. Annu Rev Pathol. 2006;1:331–48.
Woo HG, Choi JH, Yoon S, Jee BA, Cho EJ, Lee JH, Yu SJ, Yoon JH, Yi NJ, Lee KW, Suh KS, Kim YJ. Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer. Nat Commun. 2017;8:839.
Wu B, Wang Z, Lin N, Yan XB, Lv ZC, Ying ZM, Ye ZM. A panel of eight mRNA signatures improves prognosis prediction of osteosarcoma patients. Medicine. 2021a;100:e24118.
Wu L, Liu F, Cai H. IOAT: an interactive tool for statistical analysis of omics data and clinical data. BMC Bioinformatics. 2021b;22:326.
Wu Y, Yang Y, Gu H, Tao B, Zhang E, Wei J, Wang Z, Liu A, Sun R, Chen M, Fan Y, Mao R. Multi-omics analysis reveals the functional transcription and potential translation of enhancers. Int J Cancer. 2020;147:2210–24.
Xie B, Yuan Z, Yang Y, Sun Z, Zhou S, Fang X. MOBCdb: a comprehensive database integrating multi-omics data on breast cancer for precision medicine. Breast Cancer Res Treat. 2018;169:625–32.
Xie Q, Fan F, Wei W, Liu Y, Xu Z, Zhai L, Qi Y, Ye B, Zhang Y, Basu S, Zhao Z, Wu J, Xu P. Multi-omics analyses reveal metabolic alterations regulated by hepatitis B virus core protein in hepatocellular carcinoma cells. Sci Rep. 2017;7:41089.
Xie Y. Hepatitis B virus-associated hepatocellular carcinoma. Adv Exp Med Biol. 2017;1018:11–21.
Xu Q, Zhai JC, Huo CQ, Li Y, Dong XJ, Li DF, Huang RD, Shen C, Chang YJ, Zeng XL, Meng FL, Yang F, Zhang WL, Zhang SN, Zhou YM, Zhang Z. OncoPDSS: an evidence-based clinical decision support system for oncology pharmacotherapy at the individual level. BMC Cancer. 2020a;20:740.
Xu X, Gong C, Wang Y, Hu Y, Liu H, Fang Z. Multi-omics analysis to identify driving factors in colorectal cancer. Epigenomics. 2020b;12:1633–50.
Xu Y, She Y, Li Y, Li H, Jia Z, Jiang G, Liang L, Duan L. Multi-omics analysis at epigenomics and transcriptomics levels reveals prognostic subtypes of lung squamous cell carcinoma. Biomed Pharmacother. 2020c;125:109859.
Yamashita T, Wang XW. Cancer stem cells in the development of liver cancer. J Clin Investig. 2013;123:1911–8.
Yang H, Jin W, Liu H, Wang X, Wu J, Gan D, Cui C, Han Y, Han C, Wang Z. A novel prognostic model based on multi-omics features predicts the prognosis of colon cancer patients. Mol Genet Genomic Med. 2020a;8:e1255.
Yang Z, Xu J, Li L, Li R, Wang Y, Tian Y, Guo W, Wang Z, Tan F, Ying J, Jiao Y, Gao S, Wang J, Gao Y, He J. Integrated molecular characterization reveals potential therapeutic strategies for pulmonary sarcomatoid carcinoma. Nat Commun. 2020b;11:4878.
Yi H, Li G, Long Y, Liang W, Cui H, Zhang B, Tan Y, Li Y, Shen L, Deng D, Tang Y, Mao C, Tian S, Cai Y, Zhu Q, Hu Y, Chen W, Fang L. Integrative multi-omics analysis of a colon cancer cell line with heterogeneous Wnt activity revealed RUNX2 as an epigenetic regulator of EMT. Oncogene. 2020;39:5152–64.
Yi T, Zhang Y, Ng DM, Xi Y, Ye M, Cen L, Li J, Fan X, Li Y, Hu S, Rong H, Xie Y, Zhao G, Chen L, Chen C, Ni S, Mi J, Dai X, Liao Q. Regulatory network analysis of mutated genes based on multi-omics data reveals the exclusive features in tumor immune microenvironment between left-sided and right-sided colon cancer. Front Oncol. 2021;11:685515.
Yildiz G. Integrated multi-omics data analysis identifying novel drug sensitivity-associated molecular targets of hepatocellular carcinoma cells. Oncol Lett. 2018;16:113–22.
Yin Z, Yan X, Wang Q, Deng Z, Tang K, Cao Z, Qiu T. Detecting prognosis risk biomarkers for colon cancer through multi-omics-based prognostic analysis and target regulation simulation Modeling. Front Genet. 2020;11:524.
Yoo BC, Kim KH, Woo SM, Myung JK. Clinical multi-omics strategies for the effective cancer management. J Proteome. 2018;188:97–106.
Yu C, Qi X, Lin Y, Li Y, Shen B. iODA: an integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. J Biomed Inform. 2020;112:103605.
Yuan Y, Bao J, Chen Z, Villanueva AD, Wen W, Wang F, Zhao D, Fu X, Cai Q, Long J, Shu XO, Zheng D, Moreno V, Zheng W, Lin W, Guo X. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Hum Mol Genet. 2021;30:321–30.
Zeng D, Ye Z, Shen R, Yu G, Wu J, Xiong Y, Zhou R, Qiu W, Huang N, Sun L, Li X, Bin J, Liao Y, Shi M, Liao W. IOBR: multi-omics immuno-oncology biological research to decode tumor microenvironment and signatures. Front Immunol. 2021;12:687975.
Zhang H, Jin Z, Cheng L, Zhang B. Integrative analysis of methylation and gene expression in lung adenocarcinoma and squamous cell lung carcinoma. Front Bioeng Biotechnol. 2020a;8:3.
Zhang J, Bajari R, Andric D, Gerthoffert F, Lepsa A, Nahal-Bose H, Stein LD, Ferretti V. The international cancer genome consortium data portal. Nat Biotechnol. 2019;37:367–9.
Zhang Y, Yang M, Ng DM, Haleem M, Yi T, Hu S, Zhu H, Zhao G, Liao Q. Multi-omics data analyses construct TME and identify the immune-related prognosis signatures in human LUAD. Mol Ther Nucleic Acids. 2020b;21:860–73.
Zochbauer-Muller S, Minna JD. The biology of lung cancer including potential clinical applications. Chest Surg Clin N Am. 2000;10:691–708.
Zou Y, Ruan S, Jin L, Chen Z, Han H, Zhang Y, Jian Z, Lin Y, Shi N, Jin H. CDK1, CCNB1, and CCNB2 are prognostic biomarkers and correlated with immune infiltration in hepatocellular carcinoma. Med Sci Monit. 2020;26:e925289.
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We thank all the individuals who have helped us in this study. We acknowledge the valuable work of the many investigators whose published articles we were unable to cite owing to space limitations.
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This work was financially supported by the grants from the National Natural Science Foundation of China (31861143051, 31872425, 32002235, 31602008) and Senior Talent Foundation of Jiangsu University (19JDG039).
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Zhang, H., Gong, X., Tang, M. (2023). Multi-Omics Data Analysis for Cancer Research: Colorectal Cancer, Liver Cancer and Lung Cancer. In: Ning, K. (eds) Methodologies of Multi-Omics Data Integration and Data Mining. Translational Bioinformatics, vol 19. Springer, Singapore. https://doi.org/10.1007/978-981-19-8210-1_5
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