Rawla P, Sunkara T, Barsouk A. Epidemiology of colorectal cancer: incidence, mortality, survival, and risk factors. Prz Gastroenterol. 2019;14:89–103.

CAS  PubMed  PubMed Central  Google Scholar 

van der Sijp MPL, Bastiaannet E, Mesker WE, van der Geest LGM, Breugom AJ, Steup WH, et al. Differences between colon and rectal cancer in complications, short-term survival and recurrences. Int J Colorectal Dis. 2016;31:1683–91.

Article  PubMed  PubMed Central  Google Scholar 

Hu Y, Gaedcke J, Emons G, Beissbarth T, Grade M, Jo P, et al. Colorectal cancer susceptibility loci as predictive markers of rectal cancer prognosis after surgery. Genes Chromosomes Cancer. 2018;57:140–9.

Article  CAS  PubMed  Google Scholar 

Body A, Prenen H, Latham S, Lam M, Tipping-Smith S, Raghunath A, et al. The role of neoadjuvant chemotherapy in locally advanced colon cancer. Cancer Manag Res. 2021;13:2567–79.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Seo I, Lee HW, Byun SJ, Park JY, Min H, Lee SH, et al. Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer. J Immunother Cancer. 2021;9. Available from: https://doi.org/10.1136/jitc-2020-001610

Wang W, Kandimalla R, Huang H, Zhu L, Li Y, Gao F, et al. Molecular subtyping of colorectal cancer: recent progress, new challenges and emerging opportunities. Semin Cancer Biol. 2019;55:37–52.

Article  CAS  PubMed  Google Scholar 

Guinney J, Dienstmann R, Wang X, de Reyniès A, Schlicker A, Soneson C, et al. The consensus molecular subtypes of colorectal cancer. Nat Med. 2015;21:1350–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Roepman P, Schlicker A, Tabernero J, Majewski I, Tian S, Moreno V, et al. Colorectal cancer intrinsic subtypes predict chemotherapy benefit, deficient mismatch repair and epithelial-to-mesenchymal transition. Int J Cancer. 2014;134:552–62.

Article  CAS  PubMed  Google Scholar 

Budinska E, Popovici V, Tejpar S, D’Ario G, Lapique N, Sikora KO, et al. Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer. J Pathol. 2013;231:63–76.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schlicker A, Beran G, Chresta CM, McWalter G, Pritchard A, Weston S, et al. Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines. BMC Med Genom. 2012;5:66.

Article  CAS  Google Scholar 

Sadanandam A, Lyssiotis CA, Homicsko K, Collisson EA, Gibb WJ, Wullschleger S, et al. A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med. 2013;19:619–25.

Article  CAS  PubMed  PubMed Central  Google Scholar 

De Sousa E Melo F, Wang X, Jansen M, Fessler E, Trinh A, de Rooij LPMH, et al. Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions. Nat Med. 2013;19:614–8.

Article  PubMed  Google Scholar 

Marisa L, de Reyniès A, Duval A, Selves J, Gaub MP, Vescovo L, et al. Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS Med. 2013;10:e1001453.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fontana E, Eason K, Cervantes A, Salazar R, Sadanandam A. Context matters-consensus molecular subtypes of colorectal cancer as biomarkers for clinical trials. Ann Oncol. 2019;30:520–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Song L, Langfelder P, Horvath S. Comparison of co-expression measures: mutual information, correlation, and model based indices. BMC Bioinforma. 2012;13:328.

Article  CAS  Google Scholar 

Alexa AJR. topGO [Internet]. Bioconductor; 2017. Available from: https://bioconductor.org/packages/topGO

Monti S, Tamayo P, Mesirov J, Golub T. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach Learn. 2003;52:91–118.

Article  Google Scholar 

Eide PW, Bruun J, Lothe RA, Sveen A. CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models. Sci Rep. 2017;7:16618.

Article  PubMed  PubMed Central  Google Scholar 

Isella C, Brundu F, Bellomo SE, Galimi F, Zanella E, Porporato R, et al. Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer. Nat Commun. 2017;8:15107.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Krull M, Pistor S, Voss N, Kel A, Reuter I, Kronenberg D, et al. TRANSPATH®: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 2006;34:D546–51.

Article  CAS  PubMed  Google Scholar 

Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006;34:D108–10.

Article  CAS  PubMed  Google Scholar 

Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12:453–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 2016;17:1–20.

Google Scholar 

Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.

Article  PubMed  Google Scholar 

Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, et al. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nat Commun. 2018;9:1–11.

Article  Google Scholar 

Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinforma. 2013;14:7.

Article  Google Scholar 

Merlos-Suárez A, Barriga FM, Jung P, Iglesias M, Céspedes MV, Rossell D, et al. The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse. Cell Stem Cell. 2011;8:511–24.

Article  PubMed  Google Scholar 

Gerdes MJ, Gökmen-Polar Y, Sui Y, Pang AS, LaPlante N, Harris AL, et al. Single-cell heterogeneity in ductal carcinoma in situ of breast. Mod Pathol. 2018;31:406–17.

Article  CAS  PubMed  Google Scholar 

Gerdes MJ, Sevinsky CJ, Sood A, Adak S, Bello MO, Bordwell A, et al. Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue. Proc Natl Acad Sci USA. 2013;110:11982–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lindner AU, Salvucci M, McDonough E, Cho S, Stachtea X, O’Connell EP, et al. An atlas of inter- and intra-tumor heterogeneity of apoptosis competency in colorectal cancer tissue at single-cell resolution. Cell Death Differ. 2022;29:806–17.

Article  CAS  PubMed  Google Scholar 

Paschke S, Jafarov S, Staib L, Kreuser ED, Maulbecker-Armstrong C, Roitman M, et al. Are colon and rectal cancer two different tumor entities? A proposal to abandon the term colorectal cancer. Int J Mol Sci. 2018;30:19. Available from: https://doi.org/10.3390/ijms19092577

Tamas K, Walenkamp AME, de Vries EGE, van Vugt MATM, Beets-Tan RG, van Etten B, et al. Rectal and colon cancer: not just a different anatomic site. Cancer Treat Rev. 2015;41:671–9.

Article  CAS  PubMed  Google Scholar 

Mukund K, Syulyukina N, Ramamoorthy S, Subramaniam S. Right and left-sided colon cancers - specificity of molecular mechanisms in tumorigenesis and progression. BMC Cancer. 2020;20:1–15.

Article  Google Scholar 

Xie B, Bai B, Xu Y, Liu Y, Lv Y, Gao X, et al. Tumor-suppressive function and mechanism of HOXB13 in right-sided colon cancer. Signal Transduct Target Ther. 2019;4:1–14.

CAS  Google Scholar 

Geng H, Liu G, Hu J, Li J, Wang D, Zou S, et al. HOXB13 suppresses proliferation, migration and invasion, and promotes apoptosis of gastric cancer cells through transcriptional activation of VGLL4 to inhibit the involvement of TEAD4 in the Hippo signaling pathway. Mol Med Rep. 2021;24. Available from: https://doi.org/10.3892/mmr.2021.12361

Martinou E, Falgari G, Bagwan I, Angelidi AM. A systematic review on HOX genes as potential biomarkers in colorectal cancer: an emerging role of HOXB9. Int J Mol Sci. 2021;22:13429.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng B, Rong A, Zhou Q, Li W. CLDN8 promotes colorectal cancer cell proliferation, migration, and invasion by activating MAPK/ERK signaling. Cancer Manag Res. 2019;11:3741–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fedele M, Cerchia L, Pegoraro S, Sgarra R, Manfioletti G. Proneural-mesenchymal transition: phenotypic plasticity to acquire multitherapy resistance in glioblastoma. Int J Mol Sci. 2019;4:20. Available from: https://doi.org/10.3390/ijms20112746

Kim Y, Varn FS, Park SH, Yoon BW, Park HR, Lee C, et al. Perspective of mesenchymal transformation in glioblastoma. Acta Neuropathol Commun. 2021;9:50.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Buchholz TA, Stivers DN, Stec J, Ayers M, Clark E, Bolt A, et al. Global gene expression changes during neoadjuvant chemotherapy for human breast cancer. Cancer J. 2002;8:461–8.

Article  PubMed  Google Scholar 

Kikuchi Y, Kashima TG, Nishiyama T, Shimazu K, Morishita Y, Shimazaki M, et al. Periostin is expressed in pericryptal fibroblasts and cancer-associated fibroblasts in the colon. J Histochem Cytoche