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Excavating thyroid carcinoma risk metabolic genes associated with biological clock by bioinformatics analysis: A study based on TCGA and GEO data


 Background Thyroid carcinoma (TC) is malignant tumor of the endocrine gland with a significantly increased incidence in recent years, which related to metabolic diseases and biological clock disorder. The molecular mechanism and risk metabolic genes associated with biological clock of TC require conducting study. Methods We mined differentially expressed genes of TC (TC-DEGs) from TCGA and GEO database. Searching for biorhythm related genes (BRGs) based on core clock genes by STRING analysis. Next, we used a series of bioinformatics methods to analyze the TC-DEGs and BRGs, including chromosome location, GO and KEGG pathway annotation. Then, we extracted the expression of statistically significant TC metabolic genes by Perl program combined with a computational method of GSEA. Furthermore, screen the risk metabolic genes and reveal potential underlying KEGG pathways of the gene signatures. Results Our results identified 474 DEGs (P < 0.05; |log FC| > 1) in patients with TC compared with the normal controls using the available numerical mRNA expression values. The chromosomal assignments of TC-DEGs and BRGs were inhomogeneous. These genes were mainly distributed on Chrom01, 02, 11, 12, 04, 03 and X, none of the associated genes were distributed on sex Y chromosome. ARNTL and BHLHE40 belong to both the TC-DEGs and BRGs. PER2, NCOR1, RXRG, CCND1, SERPINE1 and PLAU were mined which act as the hub of signaling pathways linking “Thyroid hormone signaling pathway”, “Circadian rhythm”, “Transcriptional misregulation in cancer” and so on. One hundred and forty-one metabolic genes were extracted to train the prognostic model, and 11 risk genes were found, among them, 10 risk gene products have indirect interaction with ARNTL and BHLHE40. Such important genes for TC were regulated by many common conserved microRNAs. Conclusions Our study identified 8 key genes and 11 risk metabolic genes of thyroid carcinoma associated with biological clock by bioinformatics analysis. And the coding products of these genes form a clear interaction network, which is conducive to further study the molecular mechanism, reveal the role of circadian clock genes and metabolic genes in thyroid cancer.