Identification of crucial regulatory relationships between long non-coding RNAs and protein-coding genes in lung squamous cell carcinoma

2016 ◽  
Vol 30 (3) ◽  
pp. 146-152 ◽  
Author(s):  
Xiaofen Wu ◽  
Lei Ruan ◽  
Yi Yang ◽  
Qi Mei
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Lung Squamous Cell Carcinoma ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rnas

scholarly journals Identification of key pathways regulated by a set of competitive long non-coding RNAs in oral squamous cell carcinoma

2019 ◽  
Vol 47 (4) ◽  
pp. 1758-1765 ◽  
Author(s):  
Zhifeng Yang ◽  
Zili Liu ◽  
Lingqiu Meng ◽  
Shuyan Ma
Keyword(s):  
Cell Cycle ◽  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rnas ◽  
Key Pathways ◽  
Competitive Endogenous Rna

Objective The aim of this study was to identify important pathways regulated by a set of long non-coding RNAs (lncRNAs) in oral squamous cell carcinoma (OSCC). Methods A lncRNA-mediated competitive endogenous RNA network (LMCN) was constructed using information on microRNA (miRNA)–mRNA interactions and lncRNA–miRNA intersections from the E-GEOD-37991 transcription profiling data in the ArrayExpress database. A random walk with restart ranking algorithm was then applied to evaluate the influences of protein-coding genes regulated by competitive lncRNAs. Pathway enrichment scores were calculated based on the propagation scores of protein-coding genes. Finally, permutation tests were used to estimate the significance of the pathways. Results We obtained lncRNA–mRNA interactions based on miRNAs common to both miRNA–mRNA interactions and lncRNA–miRNA intersections, and used interactions with a z-score > 0.7 to construct a LMCN. Ten lncRNAs were identified as source nodes in the LMCN, and nine pathways with enrichment scores >0.8, including ‘Cell cycle’, ‘Endocytosis’, and ‘Pathways in cancer’, were significantly enriched by these source nodes. Conclusions Nine significant pathways regulated by a set of competitive lncRNAs were identified in OSCC, which may play important roles in the development of OSCC via the cell cycle and endocytosis.

Protein-coding genes combined with long non-coding RNAs predict prognosis in esophageal squamous cell carcinoma patients as a novel clinical multi-dimensional signature

2016 ◽  
Vol 12 (11) ◽  
pp. 3467-3477 ◽  
Author(s):  
Jin-Cheng Guo ◽  
Chun-Quan Li ◽  
Qiu-Yu Wang ◽  
Jian-Mei Zhao ◽  
Ji-Yu Ding ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Mortality Rate ◽  
Esophageal Squamous Cell Carcinoma ◽  
Esophageal Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Gastrointestinal Cancers ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Non Coding Rnas

Esophageal carcinoma is one of the most malignant gastrointestinal cancers worldwide, and has a high mortality rate.

scholarly journals How Long Non-Coding RNAs and MicroRNAs Mediate the Endogenous RNA Network of Head and Neck Squamous Cell Carcinoma: a Comprehensive Analysis

2018 ◽  
Vol 50 (1) ◽  
pp. 332-341 ◽  
Author(s):  
Guomiao Zhao ◽  
Yaru Fu ◽  
Zhifang Su ◽  
Rongling wu
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Cancer Metastasis ◽  
Lung Squamous Cell Carcinoma ◽  
Neck Squamous Cell Carcinoma ◽  
Differentially Expressed ◽  
Clinical Prognosis ◽  
Non Coding Rnas

Background/Aims: Long non-coding RNAs (lncRNAs) act as competing endogenous RNAs (ceRNAs) to compete for microRNAs (miRNAs) in cancer metastasis. Head and neck squamous cell carcinoma (HNSCC) is one of the most common human cancers and rare biomarkers could predict the clinical prognosis of this disease and its therapeutic effect. Methods: Weighted gene co-expression network analysis (WGCNA) was performed to identify differentially expressed mRNAs (DEmRNAs) that might be key genes. GO enrichment and protein–protein interaction (PPI) analyses were performed to identify the principal functions of the DEmRNAs. An lncRNA-miRNA-mRNA network was constructed to understand the regulatory mechanisms in HNSCC. The prognostic signatures of mRNAs, miRNAs, and lncRNAs were determined by Gene Expression Profiling Interactive Analysis (GEPIA) and using Kaplan–Meier survival curves for patients with lung squamous cell carcinoma. Results: We identified 2,023 DEmRNAs, 1,048 differentially expressed lncRNAs (DElncRNAs), and 82 differentially expressed miRNAs (DEmiRNAs). We found that eight DEmRNAs, 53 DElncRNAs, and 16 DEmiRNAs interacted in the ceRNA network. Three ceRNAs (HCG22, LINC00460 and STC2) were significantly correlated with survival. STC2 transcript levels were significantly higher in tumour tissues than in normal tissues, and the STC2 expression was slightly upregulated at different stages of HNSCC. Conclusion: LINC00460, HCG22 and STC2 exhibited aberrant levels of expression and may participate in the pathogenesis of HNSCC.

A Systematic Analysis of Dysregulated Long Non-Coding RNAs/microRNAs/mRNAs in Lung Squamous Cell Carcinoma

2020 ◽  
Vol 360 (6) ◽  
pp. 701-710
Author(s):  
Tong-Jia Zhang ◽  
Jia-Shun Cao ◽  
Qiu Li ◽  
Guo-Shun An ◽  
Ju-Hua Ni ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Lung Squamous Cell Carcinoma ◽  
Systematic Analysis ◽  
Non Coding Rnas

PD-1 and PD-L1 Related Comprehensive Analysis of Lung Squamous Cell Carcinoma

2018 ◽  
Author(s):  
Guoping Li ◽  
Junyi Wang ◽  
Xi Dai ◽  
Dehong Wu ◽  
Xiang He ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Lung Squamous Cell Carcinoma ◽  
Comprehensive Analysis
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