Identification of gene co-expression modules and hub genes associated with lymph node metastasis of papillary thyroid cancer.
Papillary thyroid cancer (PTC) is the most prevalent histological type among thyroid cancers, and some patients are at a high risk for recurrent disease or even death. Identification for the potential biomarkers of PTC may contribute to early discovery of recurrence and treatment. In The Cancer Genome Atlas (TCGA) database, we obtained the information of RNA sequence data and clinical characteristics of PTC. Weighted gene co-expression network analysis (WGCNA) was performed to construct gene co-expression networks and investigate the relationship between modules and clinical traits. Finally, we constructed 16 co-expression modules in 10,428 genes, and three key modules (darkturquoise, lightyellow, and red) associated with tumor N grade were identified. The results of functional annotation indicated that the darkturquoise module was primarily enriched in the regulation of the extracellular matrix (ECM), collagen metabolism, and cell adhesion, the lightyellow module was primarily enriched in the mitochondrial function regulation and energy synthesis, and the red module was primarily enriched in the process of cell junction, apoptosis, and inflammatory response, suggesting their significant role in the progression of PTC. In addition, the hub genes in the three modules were identified and screened for differentially expressed genes (DEGs). Relapse-free survival analyses found that 11 genes (KCNQ3, MET, FN1, ITGA3, RUNX1, ITGA2, PERP, GCSH, FAAH, NGFRAP1, and HSPA5) may play a pivotal role in PTC relapse. In general, our research revealed the key co-expression modules and identified several prognostic biomarkers, which provides some new insights into the lymph node metastasis of PTC.
['Zhai|Tianyu|T|http://orcid.org/0000-0002-8899-4710', 'Muhanhali|Dilidaer|D|', 'Jia|Xi|X|', 'Wu|Zhiyong|Z|', 'Cai|Zhenqin|Z|', 'Ling|Yan|Y|']
D000293:Adolescent D000328:Adult D000368:Aged D000369:Aged, 80 and over D045744:Cell Line, Tumor D000091342:Endoplasmic Reticulum Chaperone BiP D005260:Female D053263:Gene Regulatory Networks D006801:Humans D008207:Lymphatic Metastasis D008297:Male D008875:Middle Aged D060066:Protein Interaction Maps D000077273:Thyroid Cancer, Papillary D013964:Thyroid Neoplasms D059467:Transcriptome D055815:Young Adult
Hub genes Lymph node metastasis Papillary thyroid cancer Weighted gene co-expression network analysis