Potential Novel Modules and Hub Genes as Prognostic Candidates of Thyroid Cancer by Weighted Gene Co-Expression Network Analysis

References

• Kitahara CM, Sosa JA. The changing incidence of thyroid cancer. Nat Rev Endocrinol. 2016;12(11):646–653. doi:10.1038/nrendo.2016.110
   PubMed Web of Science ®Google Scholar
• Hu J, Yuan IJ, Mirshahidi S, Simental A, Lee SC, Yuan X. Thyroid carcinoma: phenotypic features, underlying biology and potential relevance for targeting therapy. Int J Mol Sci. 2021;22(4):1950. doi:10.3390/ijms22041950
   PubMed Web of Science ®Google Scholar
• Patel S, Pappoppula L, Guddati AK, et al. Analysis of race and gender disparities in incidence-based mortality in patients diagnosed with thyroid cancer from 2000 to 2016. Int J Gen Med. 2020;13:1589–1594. doi:10.2147/IJGM.S280986
   PubMed Web of Science ®Google Scholar
• Siegel RL, Miller KD, Fuchs HE, Jemal A. Cancer statistics, 2021. CA Cancer J Clin. 2021;71(1):7–33. doi:10.3322/caac.21654
   PubMed Web of Science ®Google Scholar
• Davies L, Hoang JK. Thyroid cancer in the USA: current trends and outstanding questions. Lancet Diabetes Endocrinol. 2021;9(1):11–12. doi:10.1016/S2213-8587(20)30372-7
   PubMed Web of Science ®Google Scholar
• Chen W, Zheng R, Zuo T, Zeng H, Zhang S, He J. National cancer incidence and mortality in China, 2012. Chin J Cancer Res. 2016;28:1–11.
   PubMed Web of Science ®Google Scholar
• Davies L, Welch HG. Current thyroid cancer trends in the United States. JAMA Otolaryngol Head Neck Surg. 2014;140(4):317–322. doi:10.1001/jamaoto.2014.1
   PubMed Web of Science ®Google Scholar
• Schlumberger MJ. Papillary and follicular thyroid carcinoma. N Engl J Med. 1998;338(5):297–306. doi:10.1056/NEJM199801293380506
   PubMed Web of Science ®Google Scholar
• Mazzaferri EL, Kloos RT. Clinical review 128: current approaches to primary therapy for papillary and follicular thyroid cancer. J Clin Endocrinol Metab. 2001;86(4):1447–1463. doi:10.1210/jcem.86.4.7407
   PubMed Web of Science ®Google Scholar
• LiVolsi VA. Papillary thyroid carcinoma: an update. Mod Pathol. 2011;24(S2):S1–S9. doi:10.1038/modpathol.2010.129
   PubMed Web of Science ®Google Scholar
• Nikiforov YE, Nikiforova MN. Molecular genetics and diagnosis of thyroid cancer. Nat Rev Endocrinol. 2011;7(10):569–580. doi:10.1038/nrendo.2011.142
   PubMed Web of Science ®Google Scholar
• Giulietti M, Occhipinti G, Principato G, Piva F. Weighted gene co-expression network analysis reveals key genes involved in pancreatic ductal adenocarcinoma development. Cell Oncol. 2016;39(4):379–388. doi:10.1007/s13402-016-0283-7
   PubMed Web of Science ®Google Scholar
• Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9(1):559. doi:10.1186/1471-2105-9-559
   PubMed Web of Science ®Google Scholar
• Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005;4:Article17. doi:10.2202/1544-6115.1128
   PubMed Web of Science ®Google Scholar
• Zhou Z, Cheng Y, Jiang Y, et al. Ten hub genes associated with progression and prognosis of pancreatic carcinoma identified by co-expression analysis. Int J Biol Sci. 2018;14:124–136. doi:10.7150/ijbs.22619
   PubMed Web of Science ®Google Scholar
• Tang J, Yang Q, Cui Q, et al. Weighted gene correlation network analysis identifies RSAD2, HERC5, and CCL8 as prognostic candidates for breast cancer. J Cell Physiol. 2020;235(1):394–407. doi:10.1002/jcp.28980
   PubMed Web of Science ®Google Scholar
• Hu X, Sun G, Shi Z, Ni H, Jiang S. Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis. PeerJ. 2020;8:e8505. doi:10.7717/peerj.8505
   PubMed Web of Science ®Google Scholar
• Shi K, Bing ZT, Cao GQ, et al. Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis. Int J Ophthalmol. 2015;8:269–274.
   PubMed Web of Science ®Google Scholar
• Dennis G Jr, Sherman BT, Hosack DA, et al. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 2003;4(5):P3. doi:10.1186/gb-2003-4-5-p3
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000;25:25–29. doi:10.1038/75556
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2002;40:D109–D114. doi:10.1093/nar/gkr988
   Web of Science ®Google Scholar
• Uhlén M, Fagerberg L, Hallström BM, et al. Proteomics. Tissue-based map of the human proteome. Science. 2015;347(6220):1260419. doi:10.1126/science.1260419
   PubMed Web of Science ®Google Scholar
• Li H, Tian Z, Qu Y, et al. SIRT7 promotes thyroid tumorigenesis through phosphorylation and activation of Akt and p70S6K1 via DBC1/SIRT1 axis. Oncogene. 2019;38(3):345–359. doi:10.1038/s41388-018-0434-6
   PubMed Web of Science ®Google Scholar
• Li X, Ruan X, Zhang P, et al. TBX3 promotes proliferation of papillary thyroid carcinoma cells through facilitating PRC2-mediated p57KIP2 repression. Oncogene. 2018;37(21):2773–2792. doi:10.1038/s41388-017-0090-2
   PubMed Web of Science ®Google Scholar
• Li Y, Yang Q, Guan H, Shi B, Ji M, Hou P. ZNF677 suppresses Akt phosphorylation and tumorigenesis in thyroid cancer. Cancer Res. 2018;78(18):5216–5228. doi:10.1158/0008-5472.CAN-18-0003
   PubMed Web of Science ®Google Scholar
• Ock S, Ahn J, Lee SH, et al. Thyrocyte-specific deletion of insulin and IGF-1 receptors induces papillary thyroid carcinoma-like lesions through EGFR pathway activation. Int J Cancer. 2018;143(10):2458–2469. doi:10.1002/ijc.31779
   PubMed Web of Science ®Google Scholar
• Ren Z, Zhang L, Ding W, et al. Development and validation of a novel survival model for head and neck squamous cell carcinoma based on autophagy-related genes. Genomics. 2021;113(1):1166–1175. doi:10.1016/j.ygeno.2020.11.017
   PubMed Web of Science ®Google Scholar
• Xiao H, Zhang Y, Li Z, et al. Periostin deficiency reduces diethylnitrosamine -induced liver cancer in mice by decreasing hepatic stellate cell activation and cancer cell proliferation. J Pathol. 2021;255(2):212–223. doi:10.1002/path.5756
   PubMed Web of Science ®Google Scholar
• Yuan Y, Cao W, Zhou H, Qian H, Wang H. H2A.Z acetylation by lincZNF337-AS1 via KAT5 implicated in the transcriptional misregulation in cancer signaling pathway in hepatocellular carcinoma. Cell Death Dis. 2021;12(6):609. doi:10.1038/s41419-021-03895-2
   PubMed Web of Science ®Google Scholar
• Pogorzelska-Dyrbus J, Szepietowski JC. Adhesion molecules in non-melanoma skin cancers: a comprehensive review. In Vivo (Brooklyn). 2021;35:1327–1336. doi:10.21873/invivo.12385
   Web of Science ®Google Scholar
• Gerber JM, Gucwa JL, Esopi D, et al. Genome-wide comparison of the transcriptomes of highly enriched normal and chronic myeloid leukemia stem and progenitor cell populations. Oncotarget. 2013;4(5):715–728. doi:10.18632/oncotarget.990
   PubMed Web of Science ®Google Scholar
• Xiao W, Wang X, Wang T, Xing J. MiR-223-3p promotes cell proliferation and metastasis by downregulating SLC4A4 in clear cell renal cell carcinoma. Aging. 2019;11(2):615–633. doi:10.18632/aging.101763
   PubMedGoogle Scholar
• Chen X, Chen J, Feng Y, Guan W. Prognostic value of SLC4A4 and its correlation with immune infiltration in colon adenocarcinoma. Med Sci Monit. 2020;26:e925016. doi:10.12659/MSM.925016
   PubMed Web of Science ®Google Scholar
• Guijo M, Ceballos-Chávez M, Gómez-Marín E, Basurto-Cayuela L, Reyes JC. Expression of TDRD9 in a subset of lung carcinomas by CpG island hypomethylation protects from DNA damage. Oncotarget. 2018;9(11):9618–9631. doi:10.18632/oncotarget.22709
   PubMedGoogle Scholar
• Wang Z, Liu W, Chen C, Yang X, Luo Y, Zhang B. Low mutation and neoantigen burden and fewer effector tumor infiltrating lymphocytes correlate with breast cancer metastasization to lymph nodes. Sci Rep. 2019;9(1):253. doi:10.1038/s41598-018-36319-x
   PubMed Web of Science ®Google Scholar