Identifying Effective Pathways and Genes in Colorectal Cancer according to Stage by Analyzing RNA Sequencing Data

1. World Health Organisation. colorectal
cancer; 2023 [Available from: https://
www.who.int/news-room/fact-sheets/
detail/colorectal-cancer.
2. Arnold M, Abnet CC, Neale RE,
Vignat J, Giovannucci EL, McGlynn
KA, et al. Global burden of 5 major
types of gastrointestinal cancer.
Gastroenterology. 2020;159(1):335-
49. e15.
3. Levin B. the US Multi-Society Task
Force; the American College of
Radiology Colon Cancer Committee
Screening and surveillance for the
early detection of colorectal cancer
and adenomatous polyps, 2008: a joint
guideline from the American Cancer
Society, the US Multi-Society Task
Force on Colorectal Cancer, and the
American College of Radiology. CA
Cancer J Clin. 2008;58:130-60.
4. Johns LE, Houlston RS. A systematic
review and meta-analysis of
familial colorectal cancer risk.
Official journal of the American
College of Gastroenterology| ACG.
2001;96(10):2992-3003.
5. Martinez-Useros J, Garcia-Foncillas
J. Obesity and colorectal cancer:
molecular features of adipose tissue.
Journal of translational medicine.
2016;14(1):21.
6. Santarelli RL, Pierre F, Corpet
DE. Processed meat and colorectal
cancer: a review of epidemiologic and
experimental evidence. Nutrition and
cancer. 2008;60(2):131-44.
7. Botteri E, Iodice S, Bagnardi
V, Raimondi S, Lowenfels AB,
Maisonneuve P. Smoking and
colorectal cancer: a meta-analysis.
Jama. 2008;300(23):2765-78.
8. American Cancer Society. Colorectal
Cancer Stages: The American Cancer
Society medical and editorial content
team; 2024 [Available from: https://
www.cancer.org/cancer/types/colonrectal-
cancer/detection-diagnosisstaging/
staged.html.
9. National Cancer Institute. Cancer
Stat Facts: Colorectal Cancer; 2021
[Available from: https://seer.cancer.
gov/statfacts/html/colorect.html.
10. Sun G, Li Y, Peng Y, Lu D, Zhang
F, C ui X , e t a l. I dentification o f
differentially expressed genes and
biological characteristics of colorectal
cancer by integrated bioinformatics
analysis. Journal of cellular
physiology. 2019;234(9):15215-24.
11. Chen L, Lu D, Sun K, Xu Y, Hu P, Li
X, et al. Identification of biomarkers
associated with diagnosis and
prognosis of colorectal cancer patients
based on integrated bioinformatics
analysis. Gene. 2019;692:119-25.
12. Liang B, Li C, Zhao J. Identification of
key pathways and genes in colorectal
cancer using bioinformatics analysis.
Medical Oncology. 2016;33(10):111.
13. Zeng X, Shi G, He Q, Zhu P. Screening
and predicted value of potential
biomarkers for breast cancer using
bioinformatics analysis. Scientific
reports. 2021;11(1):20799.
14. Pan H, Pan J, Song S, Ji L, Lv
H, Yang Z. Identification and
development of long non‐coding
RNA‐associated regulatory network
in colorectal cancer. Journal of
Cellular and Molecular Medicine.
2019;23(8):5200-10.
15. Huang DW, Sherman BT, Tan
Q, Kir J, Liu D, Bryant D, et al.
DAVID Bioinformatics Resources:
expanded annotation database
and novel algorithms to better
extract biology from large gene
lists. Nucleic acids research.
2007;35(suppl_2):W169-W75.
16. Kanehisa M, Furumichi M, Tanabe
M, Sato Y, Morishima K. KEGG: new
perspectives on genomes, pathways,
diseases and drugs. Nucleic acids
research. 2017;45(D1):D353-D61.
17. Shannon P, Markiel A, Ozier O,
Baliga NS, Wang JT, Ramage D, et
al. Cytoscape: a software environment
for integrated models of biomolecular
interaction networks. Genome
research. 2003;13(11):2498-504.
18. Chin C-H, Chen S-H, Wu H-H, Ho
C-W, Ko M-T, Lin C-Y. cytoHubba:
identifying hub objects and subnetworks
from complex interactome.
BMC systems biology. 2014;8:1-7.
19. Chandrashekar DS, Karthikeyan
SK, Korla PK, Patel H, Shovon AR,
Athar M, et al. UALCAN: An update
to the integrated cancer data analysis
platform. Neoplasia. 2022;25:18-27.
20. Schatoff EM, Leach BI, Dow LE.
Wnt signaling and colorectal cancer.
Current colorectal cancer reports.
2017;13(2):101-10.
21. Razi S, Noveiry BB, Keshavarz-Fathi
M, Rezaei N. IL-17 and colorectal
cancer: From carcinogenesis to
treatment. Cytokine. 2019;116:7-12.
22. Brown D, Anderton B, Wylie C.
The organization of intermediate
filaments in normal human colonic
epithelium and colonic carcinoma
cells. International Journal of Cancer.
1983;32(2):163-9.
23. Rady M, Ashraf A, Abdelaziz H,
El-Azizi M. Adaptive immune
changes in colorectal cancer: a focus
on T and B cell activation genes.
Discover Oncology. 2025;16(1):1032.
24. Kumar S, Shah JP, Bryant CS,
Imudia AN, Ali-Fehmi R, Malone
JM, et al. Prognostic significance of
keratinization in squamous cell cancer
of uterine cervix: a population based
study. Archives of gynecology and
obstetrics. 2009;280:25-32.
25. Zheng Z, Wieder T, Mauerer B, Schäfer
L, Kesselring R, Braumüller H. T
cells in colorectal cancer: unravelling
the function of different T cell subsets
in the tumor microenvironment.
International journal of molecular
sciences. 2023;24(14):11673.
26. Coppola A, Arriga R, Lauro D, Del
Principe MI, Buccisano F, Maurillo
L, et al. NK cell inflammation in
the clinical outcome of colorectal
carcinoma. Frontiers in medicine.
2015;2:33.
27. Xu N, Bradley L, Ambdukar I,
Gutkind JS. A mutant alpha subunit
of G12 potentiates the eicosanoid
pathway and is highly oncogenic
in NIH 3T3 cells. Proceedings of
the National Academy of Sciences.
1993;90(14):6741-5.
28. Daaka Y. G proteins in cancer: the
prostate cancer paradigm. Science’s
STKE. 2004;2004(216):re2-re.
29. Greenhough A, Smartt HJ, Moore
AE, Roberts HR, Williams AC,
Paraskeva C, et al. The COX-2/PGE
2 pathway: key roles in the hallmarks
of cancer and adaptation to the tumour
microenvironment. Carcinogenesis.
2009;30(3):377-86.
30. Lappano R, Maggiolini M. GPCRs
and cancer. Acta pharmacologica
sinica. 2012;33(3):351-62.
31. He X, Semenov M, Tamai K, Zeng X.
LDL receptor-related proteins 5 and
6 in Wnt/β-catenin signaling: arrows
point the way. 2004.
32. Clevers H. Wnt/β-catenin signaling
in development and disease. Cell.
2006;127(3):469-80.
33. Cabrero-de Las Heras S, Martínez-
Balibrea E. CXC family of chemokines
as prognostic or predictive biomarkers
and possible drug targets in
colorectal cancer. World journal of
gastroenterology. 2018;24(42):4738.
34. Jones SA, Wolf M, Qin S, Mackay
CR, Baggiolini M. Different functions
for the interleukin 8 receptors (IL-8R)
of human neutrophil leukocytes:
NADPH oxidase and phospholipase
D are activated through IL-8R1
but not IL-8R2. Proceedings of
the National Academy of Sciences.
1996;93(13):6682-6.
References 35. Cambier S, Gouwy M, Proost P. The
chemokines CXCL8 and CXCL12:
molecular and functional properties,
role in disease and efforts towards
pharmacological intervention.
Cellular & molecular immunology.
2023;20(3):217-51.
36. Janssens R, Struyf S, Proost
P. The unique structural and
functional features of CXCL12.
Cellular & molecular immunology.
2018;15(4):299-311.
37. Janssens R, Struyf S, Proost P.
Pathological roles of the homeostatic
chemokine CXCL12. Cytokine &
growth factor reviews. 2018;44:51-68.
38. Watanabe E, Wada T, Okekawa A,
Kitamura F, Komatsu G, Onogi Y,
et al. Stromal cell-derived factor 1
(SDF1) attenuates platelet-derived
growth factor-B (PDGF-B)-induced
vascular remodeling for adipose tissue
expansion in obesity. Angiogenesis.
2020;23:667-84.
39. Xiong L, Wei Y, Zhou X, Dai P, Cai
Y, Zhou X, et al. AGTR1 inhibits the
progression of lung adenocarcinoma.
Cancer Management and Research.
2021:8535-50.
40. Chen J, Chen J-K, Harris RC.
Angiotensin II induces epithelialto-
mesenchymal transition in renal
epithelial cells through reactive
oxygen species/Src/caveolin-mediated
activation of an epidermal growth
factor receptor–extracellular signalregulated
kinase signaling pathway.
Molecular and cellular biology.
2012;32(5):981-91.
41. Chen W, Chen Y, Zhang K, Yang W,
Li X, Zhao J, et al. AGT serves as a
potential biomarker and drives tumor
progression in colorectal carcinoma.
International immunopharmacology.
2021;101:108225.
42. Galamb O, Sipos F, Solymosi N,
Spisák S, Krenács T, Tóth K, et
al. Diagnostic mRNA expression
patterns of inflamed, benign, and
malignant colorectal biopsy specimen
and their correlation with peripheral
blood results. Cancer Epidemiology
Biomarkers & Prevention.
2008;17(10):2835-45.
43. Yagi T, Kubota E, Koyama H,
Tanaka T, Kataoka H, Imaeda K, et
al. Glucagon promotes colon cancer
cell growth via regulating AMPK
and MAPK pathways. Oncotarget.
2018;9(12):10650.
44. Ferjoux G, Bousquet C, Cordelier P,
Benali N, Lopez F, Rochaix P, et al.
Signal transduction of somatostatin
receptors negatively controlling cell
proliferation. Journal of Physiology-
Paris. 2000;94(3-4):205-10.
45. Susini C, Buscail L. Rationale for
the use of somatostatin analogs as
antitumor agents. Annals of Oncology.
2006;17(12):1733-42.
46. Spano P, Govoni S, Trabucchi M.
Studies on the pharmacological
properties of dopamine receptors in
various areas of the central nervous
system. Advances in biochemical
psychopharmacology. 1978;19:155-65.
47. Andersen PH, Gingrich JA, Bates MD,
Dearry A, Falardeau P, Senogles SE,
et al. Dopamine receptor subtypes:
beyond the D1/D2 classification.
Trends in pharmacological sciences.
1990;11(6):231-6.
48. Vallone D, Picetti R, Borrelli
E. Structure and function of
dopamine receptors. Neuroscience
& biobehavioral reviews.
2000;24(1):125-32