Identification of Commonly Dysregulated Genes in Non-small-cell Lung Cancer by Integrated Analysis of Microarray Data and qRT-PCR Validation

Tian, Ziqiang; Li, Zhenhua; Su, Wen Pang; Zhang, Yue‐Feng; Li, Yong; Cheng, Jingge; Wang, Guiying

doi:10.1007/s00408-015-9726-6

Cited by 30 publications

(31 citation statements)

References 37 publications

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“…Previous meta-analyses on NSCLC have mainly focused on either DEGs between NSCLC and normal controls (12)(13)(14) or those among different clinical stages of NSCLC (15,16). In the present analysis, however, the objective was to compare the differential expression profile between AC and SCC of NSCLC.…”

Section: Identification Of Differentially-expressed Genes Betweenmentioning

confidence: 95%

Identification of differentially-expressed genes between early-stage adenocarcinoma and squamous cell carcinoma lung cancer using meta-analysis methods

et al. 2017

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Abstract. Lung adenocarcinoma (AC) and squamous cell lung carcinoma (SCC) are two major subtypes of non-small cell lung cancer (NSCLC). Previous studies have demonstrated that fundamental differences exist in the underlying mechanisms of tumor development, growth and invasion between these subtypes. The investigation of differentially-expressed genes (DEGs) between these two NSCLC subtypes is useful for determining and understanding such differences. The present study aimed to identify those DEGs using meta-analysis and the data from four microarray experiments, consisting of 164 AC and 161 SCC samples. Raw gene expression values were converted into the probability of expression (POE) representing the differentially-expressed probability of a gene and expression barcode values representing its expression status. The results indicated that when applying a meta-analysis using barcode values, heterogeneity in genes across studies was less severe than when applying a meta-analysis using POE values. DEGs in each meta-analysis method overlapped substantially (P=1.3x10 -4 ), but the barcode method yielded a lower global false discovery rate. Based on this and several other performance statistics, it was concluded that the barcode approach outperformed the POE method. Finally, using those DEGs, ontology and pathway analyses were conducted. A number of genes and enriched pathways were found to be closely associated with NSCLC.

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Section: Identification Of Differentially-expressed Genes Betweenmentioning

confidence: 95%

Identification of differentially-expressed genes between early-stage adenocarcinoma and squamous cell carcinoma lung cancer using meta-analysis methods

et al. 2017

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“…Numerous studies attribute a significant role for collagen type I, a major constituent of stroma, on cancer cell motile properties and EMT (Sherman‐Baust et al, ; Shintani et al, ; Kirkland, ; Martins et al, ; Iseri et al, ; Li et al, ; Cheng and Leung, ; Chen et al, ; Januchowski et al, ). Indeed, the remodeling of collagen‐I enriched ECM with the evolution of the “desmoplastic reaction” is a “hallmark of majority of cancer types including pancreatic ductal adenocarcinoma” (Shields et al, ; Tian et al, ).…”

Section: Ecm Remodeling During Carcinogenesismentioning

confidence: 99%

Role of the extracellular matrix in cancer‐associated epithelial to mesenchymal transition phenomenon

Tzanakakis

Kavasi

Voudouri

et al. 2017

Developmental Dynamics

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The epithelial to mesenchymal transition (EMT) program is a crucial component in the processes of morphogenesis and embryonic development. The transition of epithelial to mesenchymal phenotype is associated with numerous structural and functional changes, including loss of cell polarity and tight cell-cell junctions, the acquisition of invasive abilities, and the expression of mesenchymal proteins. The switch between the two phenotypes is involved in human pathology and is crucial for cancer progression. Extracellular matrices (ECMs) are multi-component networks that surround cells in tissues. These networks are obligatory for cell survival, growth, and differentiation as well as tissue organization. Indeed, the ECM suprastructure, in addition to its supportive role, can process and deliver a plethora of signals to cells, which ultimately regulate their behavior. Importantly, the ECM derived signals are critically involved in the process of EMT during tumorigenesis. This review discusses the multilayer interaction between the ECM and the EMT process, focusing on contributions of discrete mediators, a strategy that may identify novel potential target molecules. Developmental Dynamics 247:368-381, 2018. V C 2017 Wiley Periodicals, Inc.

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“…More than 80% of lung cancer are non-small cell lung cancer (NSCLC) (2,3). In China, the incidence of lung cancer in the past few decades has doubled due to the aging population, smoking and decline in air quality (4).…”

Section: Introductionmentioning

confidence: 99%

Identification of miRNAs and differentially expressed genes in early phase non-small cell lung cancer

Tian

Liu²,

Pei

et al. 2016

Oncology Reports

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Abstract.To explore the potential therapeutic targets of early-stage non-small cell lung cancer (NSCLC), gene microarray analysis was conducted. The microarray data of NSCLC in stage IA, IB, IIA, and IIB (GSE50081), were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in IB vs. IA, IIA vs. IB, IIB vs. IIA were screened out via R. ToppGene Suite was used to get the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the DEGs. The GeneCoDis3 database and Cytoscape software were used to construct the transcriptional regulatory network. In total, 25, 17 and 14 DEGs were identified in IB vs. IA, IIA vs. IB, IIB vs. IIA of NSCLC, respectively. Some GO terms and pathways (e.g., extracellular space, alveolar lamellar body, bioactivation via cytochrome P450 pathway) were found significantly enriched in DEGs. Genes S100P, ALOX15B, CCL11, NLRP2, SERPINA3, FoxO4 and hsa-miR-491 may play important roles in the development of early-stage NSCLC. Thus, by bioinformatics analysis the key genes and biological processes involving in the development of early-stage NSCLC could be established, providing more potential references for the therapeutic targets.

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Identification of Commonly Dysregulated Genes in Non-small-cell Lung Cancer by Integrated Analysis of Microarray Data and qRT-PCR Validation

Cited by 30 publications

References 37 publications

Identification of differentially-expressed genes between early-stage adenocarcinoma and squamous cell carcinoma lung cancer using meta-analysis methods

Identification of differentially-expressed genes between early-stage adenocarcinoma and squamous cell carcinoma lung cancer using meta-analysis methods

Role of the extracellular matrix in cancer‐associated epithelial to mesenchymal transition phenomenon

Identification of miRNAs and differentially expressed genes in early phase non-small cell lung cancer

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