19 December 2019 : Clinical Research
Identification of Long Non-Coding RNA Expression Profiles and Co-Expression Genes in Thyroid Carcinoma Based on The Cancer Genome Atlas (TCGA) Database
Yun Zhang1B, Taobo Jin1C, Haipeng Shen1D, Junfeng Yan1E, Ming Guan1F, Xin Jin1AG*DOI: 10.12659/MSM.917845
Med Sci Monit 2019; 25:9752-9769
Abstract
BACKGROUND: Thyroid carcinoma is a malignancy with high morbidity and mortality. Genetic alterations play pivot roles in the pathogenesis of thyroid carcinoma, where long noncoding RNA (lncRNA) have been identified to be crucial. This study sought to investigate the biological functions of lncRNA expression profiles in thyroid carcinoma.
MATERIAL AND METHODS: The lncRNAs expression profiles were acquired from The Cancer Genome Atlas (TCGA) database according to 510 thyroid cancer tissues and 58 normal thyroid tissues. By using R package edgeR, differentially expressed RNAs were obtained. Also, an overall survival model was established based on Cox regression and clinical data then testified by Kaplan-Meier plot, receiver operating characteristic (ROC)-curve and C-index analysis. We investigated the co-expressed genes with lncRNAs involved in the prognostic model, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted R package clusterProfile.
RESULTS: A total of 352 lncRNAs were identified as differentially expressed in thyroid carcinoma, and an overall survival model consisting of 8 signature lncRNAs was proposed (ROC=0.862, C-index=0.893, P<0.05), 3 of which (DOCK9-DT, FAM111A-DT, and LINC01736) represent co-expressed mRNAs. However, as an oncogene, only FAM111A-DT increased the prognostic risk in thyroid carcinoma. Furthermore, we found differential genes LINC01016, LHX1-DT, IGF2-AS, ND MIR1-1HG-AS1, significantly related to lymph node metastasis (P<0.05).
CONCLUSIONS: In this study, we clarified the differential lncRNA expression profiles which were related to the tumorigenesis and prognosis in thyroid carcinoma. Our results provide new rationale and understandings to the pathogenesis and regulatory mechanisms of thyroid carcinoma.
Keywords: carcinogenesis, RNA, Long Noncoding, Databases, Genetic, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, gene ontology, Gene Regulatory Networks, Kaplan-Meier Estimate, MicroRNAs, Prognosis, Proportional Hazards Models, RNA, Messenger, ROC Curve, Receptors, Virus, Survival Analysis, transcriptome
Editorial
01 May 2022 : Editorial
Editorial: Cardiovascular Complications at One Year After SARS-CoV-2 Infection are Independent of Underlying Cardiovascular Risk Factors or Severity of COVID-19DOI: 10.12659/MSM.937048
Med Sci Monit 2022; 28:e937048
SARS-CoV-2/COVID-19
04 May 2022 : Clinical Research
Effects of Wearing Face Masks on Exercise Capacity and Ventilatory Anaerobic Threshold in Healthy Subjects ...Med Sci Monit In Press; DOI: 10.12659/MSM.936069
22 April 2022 : Clinical Research
Factors Associated with Falls During Hospitalization for Coronavirus Disease 2019 (COVID-19)Med Sci Monit In Press; DOI: 10.12659/MSM.936547
27 April 2022 : Meta-Analysis
Effect of the COVID-19 Pandemic on Serum Vitamin D Levels in People Under Age 18 Years: A Systematic Review...Med Sci Monit In Press; DOI: 10.12659/MSM.935823
06 May 2022 : Clinical Research
COVID-19: Another Cause of Dental Anxiety?Med Sci Monit 2022; 28:e936535
In Press
19 May 2022 : Clinical Research
Association Between Serum Homocysteine Levels and Severity of Diabetic Kidney Disease in 489 Patients with ...Med Sci Monit In Press; DOI: 10.12659/MSM.936323
18 May 2022 : Clinical Research
Physical and Psychosocial Concept Domains Related to Health-Related Quality of Life (HRQL) in 50 Girls and ...Med Sci Monit In Press; DOI: 10.12659/MSM.936801
18 May 2022 : Clinical Research
Association Between Variants of the Mannose-Binding Lectin 2 Gene and Susceptibility to Sepsis in the Haina...Med Sci Monit In Press; DOI: 10.12659/MSM.936134
17 May 2022 : Clinical Research
Clinical Application of C-TIRADS Category and Contrast-Enhanced Ultrasound in Differential Diagnosis of Sol...Med Sci Monit In Press; DOI: 10.12659/MSM.936368
Most Viewed Current Articles
30 Dec 2021 : Clinical Research
Retrospective Study of Outcomes and Hospitalization Rates of Patients in Italy with a Confirmed Diagnosis o...DOI :10.12659/MSM.935379
Med Sci Monit 2021; 27:e935379
08 Mar 2022 : Review article
A Review of the Potential Roles of Antioxidant and Anti-Inflammatory Pharmacological Approaches for the Man...DOI :10.12659/MSM.936292
Med Sci Monit 2022; 28:e936292
01 Nov 2020 : Review article
Long-Term Respiratory and Neurological Sequelae of COVID-19DOI :10.12659/MSM.928996
Med Sci Monit 2020; 26:e928996
01 Jan 2022 : Editorial
Editorial: Current Status of Oral Antiviral Drug Treatments for SARS-CoV-2 Infection in Non-Hospitalized Pa...DOI :10.12659/MSM.935952
Med Sci Monit 2022; 28:e935952