title: Bioinformatics analyses of significant prognostic risk markers for thyroid papillary carcinoma.
abstract: This study was aimed to identify the prognostic risk markers for thyroid papillary carcinoma (TPC) by bioinformatics. The clinical data of TPC and their microRNAs (miRNAs) and genes expression profile data were downloaded from The Cancer Genome Atlas. Elastic net-Cox's proportional regression hazards model (EN-COX) was used to identify the prognostic associated factors. The receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) curve were used to screen the significant prognostic risk miRNA and genes. Then, the target genes of the obtained miRNAs were predicted followed by function prediction. Finally, the significant risk genes were performed literature mining and function analysis. Total 1046 miRNAs and 20531 genes in 484 cases samples were identified after data preprocessing. From the EN-COX model, 30 prognostic risk factors were obtained. Based on the 30 risk factors, 3 miRNAs and 11 genes were identified from the ROC and KM curves. The target genes of miRNA-342 such as B-cell CLL/lymphoma 2 (BCL2) were mainly enriched in the biological process related to cellular metabolic process and Disease Ontology terms of lymphoma. The target genes of miRNA-93 were mainly enriched in the pathway of G1 phase. Among the 11 prognostic risk genes, v-maf avian musculoaponeurotic fibrosarcoma oncogene homologue F (MAFF), SRY (sex-determining region Y)-box 4 (SOX4), and retinoic acid receptor, alpha (RARA) encoded transcription factors. Besides, RARA was enriched in four pathways. These prognostic markers such as miRNA-93, miRNA-342, RARA, MAFF, SOX4, and BCL2 may be used as targets for TPC chemoprevention.
authors.affiliation: Department of Ophthalmology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, Peoples Republic of China.
authors.forename: Xiao-Shan
authors.initials: XS
authors.lastname: Min
authors.affiliation: Department of General Surgery, Xiangya Hospital of Central South University, #87 Xiangya Road, Changsha, Hunan, 410008, Peoples Republic of China.
authors.forename: Peng
authors.initials: P
authors.lastname: Huang
authors.affiliation: Department of General Surgery, Xiangya Hospital of Central South University, #87 Xiangya Road, Changsha, Hunan, 410008, Peoples Republic of China.
authors.forename: Xu
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of General Surgery, Xiangya Hospital of Central South University, #87 Xiangya Road, Changsha, Hunan, 410008, Peoples Republic of China.
authors.forename: Chao
authors.initials: C
authors.lastname: Dong
authors.affiliation: Department of General Surgery, Xiangya Hospital of Central South University, #87 Xiangya Road, Changsha, Hunan, 410008, Peoples Republic of China.
authors.forename: Xiao-Lin
authors.initials: XL
authors.lastname: Jiang
authors.affiliation: Department of General Surgery, Xiangya Hospital of Central South University, #87 Xiangya Road, Changsha, Hunan, 410008, Peoples Republic of China.
authors.forename: Zheng-Tai
authors.initials: ZT
authors.lastname: Yuan
authors.affiliation: Department of General Surgery, Xiangya Hospital of Central South University, #87 Xiangya Road, Changsha, Hunan, 410008, Peoples Republic of China.
authors.forename: Lin-Feng
authors.initials: LF
authors.lastname: Mao
authors.affiliation: Department of General Surgery, Xiangya Hospital of Central South University, #87 Xiangya Road, Changsha, Hunan, 410008, Peoples Republic of China. shichchchhc@163.com.
authors.forename: Shi
authors.initials: S
authors.lastname: Chang
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D002291:Carcinoma, Papillary / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D016022:Case-Control Studies; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D009367:Neoplasm Staging; D011379:Prognosis; D016016:Proportional Hazards Models; D012372:ROC Curve; D015996:Survival Rate; D013961:Thyroid Gland / Q000378:metabolism*; D013964:Thyroid Neoplasms / Q000235:genetics* / Q000401:mortality / Q000473:pathology
chemical_list: D014408:Biomarkers, Tumor; D035683:MicroRNAs
keywords: Function prediction; Prognostic risk gene; Prognostic risk microRNA; Target gene; Thyroid papillary carcinoma