A recurrence model for laryngeal cancer based on SVM and gene function clustering. (4th May 2017)

• Record Type: Journal Article
• Authors: Su, Jili; Zhang, Yanqiu; Su, Haodong; Zhang, Chuanhai; Li, Wei
• Is Part Of: Acta oto-laryngologica. Volume 137:Number 5(2017)
• Page Start: 557
• Page End: 562
• Publication Date: 2017-05-04
• Subjects: Laryngeal cancer -- differentially expressed genes -- feature genes -- survival analysis -- support vector machine; Otolaryngology -- Periodicals; Ear -- Diseases -- Periodicals; Throat -- Diseases -- Periodicals; Otolaryngology -- Electronic Resources; Otorhinolaryngologic Diseases; 617.8
• DOI: 10.1080/00016489.2016.1247984
• Languages: English
• ISSNs: 0001-6489

Abstract

Abstract: Conclusion: A prognostic model was obtained for LC. Several critical genes were unveiled. They could be potentially applied for LC recurrence prediction. Objective: Gene expression data of laryngeal cancer (LC) were analyzed to identify critical genes associated with recurrence. Methods: Two gene expression datasets were downloaded from the Gene Expression Omnibus. Dataset GSE27020 is used as the training set, containing 75 non-recurred LC cases and 34 recurred LC cases. Results: A total of 725 DEGs were identified from the training set. A total of 4126 gene pairs showed significant correlations in non-recurred LC only, corresponding to 533 genes. A total of 7235 gene pairs showed significant correlations in recurred LC only, corresponding to 608 genes. Besides, 1694 gene pairs showed significant correlations in both non-recurred and recurred LC, corresponding to 322 genes. Functional enrichment analysis was performed for the three groups of DEGs. Seven overlapping biological functions were revealed: positive regulation of chondrocyte differentiation, autoimmune thyroid disease, focal adhesion, linoleic acid metabolism, drug metabolism, organic cation transport, and ECM-receptor interaction. Eight feature genes (PDIA3, MYH11, PDK1, SDC3, RPE65, LAMC3, BTK, and UPK1B) were identified. Their prognostic effect was validated by independent test set as well as survival analysis.