scholarly journals Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma

2015 ◽  
Vol 8 (1) ◽  
Author(s):  
Vinay Randhawa ◽  
Vishal Acharya
Keyword(s):  
Squamous Cell Carcinoma ◽  
Logistic Regression ◽  
Network Analysis ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Regression Modeling ◽  
Integrated Network ◽  
Logistic Regression Modeling

scholarly journals Identification and validation of key modules and hub genes associated with the pathological stage of oral squamous cell carcinoma by weighted gene co-expression network analysis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8505 ◽  
Author(s):  
Xuegang Hu ◽  
Guanwen Sun ◽  
Zhiqiang Shi ◽  
Hui Ni ◽  
Shan Jiang
Keyword(s):  
Squamous Cell Carcinoma ◽  
Network Analysis ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Molecular Mechanisms ◽  
Pearson Correlation ◽  
Gene Set Enrichment Analysis ◽  
Hub Genes ◽  
T Stage

Background Oral squamous cell carcinoma (OSCC) is a major lethal malignant cancer of the head and neck region, yet its molecular mechanisms of tumourigenesis are still unclear. Patients and methods We performed weighted gene co-expression network analysis (WGCNA) on RNA-sequencing data with clinical information obtained from The Cancer Genome Atlas (TCGA) database. The relationship between co-expression modules and clinical traits was investigated by Pearson correlation analysis. Furthermore, the prognostic value and expression level of the hub genes of these modules were validated based on data from the TCGA database and other independent datasets from the Gene Expression Omnibus (GEO) database and the Human Protein Atlas database. The significant modules and hub genes were also assessed by functional analysis and gene set enrichment analysis (GSEA). Results We found that the turquoise module was strongly correlated with pathologic T stage and significantly enriched in critical functions and pathways related to tumourigenesis. PPP1R12B, CFD, CRYAB, FAM189A2 and ANGPTL1 were identified and statistically validated as hub genes in the turquoise module and were closely implicated in the prognosis of OSCC. GSEA indicated that five hub genes were significantly involved in many well-known cancer-related biological functions and signaling pathways. Conclusion In brief, we systematically discovered a co-expressed turquoise module and five hub genes associated with the pathologic T stage for the first time, which provided further insight that WGCNA may reveal the molecular regulatory mechanism involved in the carcinogenesis and progression of OSCC. In addition, the five hub genes may be considered candidate prognostic biomarkers and potential therapeutic targets for the precise early diagnosis, clinical treatment and prognosis of OSCC in the future.

Identification of Novel Key Targets and Candidate Drugs in Oral Squamous Cell Carcinoma

2020 ◽  
Vol 15 (4) ◽  
pp. 328-337
Author(s):  
Juan Liu ◽  
Xinjie Lian ◽  
Feng Liu ◽  
Xueling Yan ◽  
Chunyan Cheng ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Network Analysis ◽  
Virtual Screening ◽  
Oral Squamous Cell Carcinoma ◽  
Small Molecules ◽  
Cell Carcinoma ◽  
Candidate Genes ◽  
Squamous Cell ◽  
Drug Targets ◽  
Therapeutic Strategies

Background: Oral Squamous Cell Carcinoma (OSCC) is the most common malignant epithelial neoplasm. It is located within the top 10 ranking incidence of cancers with a poor prognosis and low survival rates. New breakthroughs of therapeutic strategies are therefore needed to improve the survival rate of OSCC harboring patients. Objective: Since targeted therapy is considered as the most promising therapeutic strategies in cancer, it is of great significance to identify novel targets and drugs for the treatment of OSCC. Methods: A series of bioinformatics approaches were launched to identify the hub proteins and their potential agents. Microarray analysis and several online functional activity network analysis were firstly utilized to recognize drug targets in OSCC. Subsequently, molecular docking was used to screen their potential drugs from the specs chemistry database. At the same time, the assessment of ligand-based virtual screening model was also evaluated. Results: In this study, two microarray data (GSE31056, GSE23558) were firstly selected and analyzed to get consensus candidate genes including 681 candidate genes. Additionally, we selected 33 candidate genes based on whether they belong to the kinases and transcription factors and further clustered candidate hub targets based on functions and signaling pathways with significant enrichment analysis by using DAVID and STRING online databases. Then, core PPI network was then identified and we manually selected GRB2 and IGF1 as the key drug targets according to the network analysis and previous references. Lastly, virtual screening was performed to identify potential small molecules which could target these two targets, and such small molecules can serve as the promising candidate agents for future drug development. Conclusion: In summary, our study might provide novel insights for understanding of the underlying molecular events of OSCC, and our discovered candidate targets and candidate agents could be used as the promising therapeutic strategies for the treatment of OSCC.

scholarly journals Application of weighted gene co-expression network analysis to identify key modules and hub genes in oral squamous cell carcinoma tumorigenesis

2018 ◽  
Vol Volume 11 ◽  
pp. 6001-6021 ◽  
Author(s):  
Xiaoqi Zhang ◽  
Hao Feng ◽  
Ziyu Li ◽  
Dongfang Li ◽  
Shanshan Liu ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Network Analysis ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Hub Genes

Role of Clinical Palpation in Evaluation of Cervical Lymph Node in Oral Squamous Cell Carcinoma

2013 ◽  
Vol 1 (2) ◽  
pp. 02-06
Author(s):  
SM Anwar Sadat ◽  
Sufia Nasrin Rita ◽  
Shoma Banik ◽  
Md Nazmul Hasan Khandker ◽  
Md Mahfuz Hossain ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Lymph Node ◽  
Oral Squamous Cell Carcinoma ◽  
Lymph Nodes ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Predictive Value ◽  
Cervical Lymph Node ◽  
Betel Quid ◽  
Cervical Lymph Nodes

A cross sectional study of 29 cases of oral squamous cell carcinoma with or without  cervical lymph node metastasis was done among Bangladeshi patients from January 2006 to December 2007. Majority of the study subjects (34.5%) belonged to the age group of 40-49 years. 58.6% of the study subjects were male, while remaining 41.4% of them were female. 51.7% of the lesions were located in the alveolar ridge where the other common sites were buccal mucosa (27.6%) and retro molar area (13.8%). Half of the study subjects (51.7%) were habituated to betel quid chewing followed by 37.9% and 10.3% were habituated to smoking and betel quid-smoking respectively. Grade I lesions was most prevalent (75.9%) in the study subjects.  Majority of cases presented with Stage IV lesions (55.2%). The sensitivity, specificity, positive predictive value, negative predictive value & accuracy of clinical palpation method for determining metastatic cervical lymph nodes were 93.33%, 64.29%, 73.68%, 90% and 79.3% respectively. Careful and repeated clinical palpation plays important role in evaluation of cervical lymph nodes though several modern techniques may help additionally in the management of oral cancer.DOI: http://dx.doi.org/10.3329/updcj.v1i2.13978 Update Dent. Coll. j. 2011: 1(2): 02-06

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