Identification of nine key genes by bioinformatics analysis for predicting poor prognosis in smoking-induced lung adenocarcinoma

Aim: To screen and identify key genes related to the development of smoking-induced lung adenocarcinoma (LUAD). Materials & methods: We obtained data from the GEO chip dataset GSE31210. The differentially expressed genes were screened by GEO2R. The protein interaction network of differentially expressed genes was constructed by STRING and Cytoscape. Finally, core genes were screened. The overall survival time of patients with the core genes was analyzed by Kaplan–Meier method. Gene ontology and Kyoto encyclopedia of genes and genomes bioaccumulation was calculated by DAVID. Results: Functional enrichment analysis indicated that nine key genes were actively involved in the biological process of smoking-related LUAD. Conclusion: 23 core genes and nine key genes among them were correlated with adverse prognosis of LUAD induced by smoking.

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Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium

BioMed Research International ◽

10.1155/2019/2767512 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 2

Author(s):

Siying He ◽

Hui Sun ◽

Yifang Huang ◽

Shiqi Dong ◽

Chen Qiao ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Gene Expression Omnibus ◽

Functional Enrichment ◽

Differentially Expressed ◽

Differentially Expressed Mirnas

Purpose. MiRNAs have been widely analyzed in the occurrence and development of many diseases, including pterygium. This study aimed to identify the key genes and miRNAs in pterygium and to explore the underlying molecular mechanisms. Methods. MiRNA expression was initially extracted and pooled by published literature. Microarray data about differentially expressed genes was downloaded from Gene Expression Omnibus (GEO) database and analyzed with the R programming language. Functional and pathway enrichment analyses were performed using the database for Annotation, Visualization and Integrated Discovery (DAVID). The protein-protein interaction network was constructed with the STRING database. The associations between chemicals, differentially expressed miRNAs, and differentially expressed genes were predicted using the online resource. All the networks were constructed using Cytoscape. Results. We found that 35 miRNAs and 301 genes were significantly differentially expressed. Functional enrichment analysis showed that upregulated genes were significantly enriched in extracellular matrix (ECM) organization, while downregulated genes were mainly involved in cell death and apoptotic process. Finally, we concluded the chemical-gene affected network, miRNA-mRNA interacted networks, and significant pathway network. Conclusion. We identified lists of differentially expressed miRNAs and genes and their possible interaction in pterygium. The networks indicated that ECM breakdown and EMT might be two major pathophysiological mechanisms and showed the potential significance of PI3K-Akt signalling pathway. MiR-29b-3p and collagen family (COL4A1 and COL3A1) might be new treatment target in pterygium.

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Based on bioinformatics analysis, NF1, BTRC and MAPK14 are the potential biomarkers in the progression of osteoarthritis synovitis

10.21203/rs.3.rs-349764/v1 ◽

2021 ◽

Author(s):

Mingyi Yang ◽

Yani Su ◽

Yao Ma ◽

Yirixiati Aihaiti ◽

Peng Xu

Keyword(s):

Differentially Expressed Genes ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Gene Expression Omnibus ◽

Functional Enrichment ◽

Differentially Expressed ◽

Hub Genes ◽

Hub Gene ◽

Potential Biomarkers

Abstract Objective: To study the potential biomarkers and related pathways in osteoarthritis (OA) synovial lesions, and to provide theoretical basis and research directions for the pathogenesis and treatment of OA. Methods: Download the microarray data sets GSE12021 and GSE82107 from Gene Expression Omnibus. GEO2R recognizes differentially expressed genes. Perform functional enrichment analysis of differentially expressed genes and construct protein-protein interaction network. Cytoscape performs module analysis and enrichment analysis of top-level modules. Further identify the Hub gene and perform functional enrichment analysis. TargetScan, miRDB and miRWalk three databases predict the target miRNAs of Hub gene and identify key miRNAs. Results: Finally, 10 Hub genes and 17 key miRNAs related to the progression of OA synovitis were identified. NF1, BTRC and MAPK14 may play a vital role in OA synovial disease. Conclusion: The Hub genes and key miRNAs discovered in this study may be potential biomarkers in the development of OA synovitis, and provide research methods and target basis for the pathogenesis and treatment of OA.

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Screening of Key Genes Associated with Ischemic Stroke via Microarray Data

Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques ◽

10.1017/s0317167100016036 ◽

2013 ◽

Vol 40 (6) ◽

pp. 864-869 ◽

Cited By ~ 2

Author(s):

Jianmin Wang ◽

Dongliang Zhou ◽

Hongwei Qin ◽

Ying Xu ◽

Ying Guan ◽

...

Keyword(s):

Ischemic Stroke ◽

Microarray Data ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Clustering Coefficient ◽

Functional Enrichment ◽

Differentially Expressed ◽

Reference Database ◽

Key Genes

Objective:To promote understandings about the pathogenesis of ischemic stroke (IS) through mining key genes, functions and pathways with microarray technology.Methods:Differentially expressed genes (DEGs) in blood between patients with IS and healthy people were screened out through comparing microarray data obtained from Gene Expression Omnibus. Overrepresented functions in DEGs were revealed by Gene Ontology (GO) enrichment analysis. Interaction network was constructed for the top 24 DEGs with information from Human Protein Reference Database (HPRD). Relevant microRNAs (miRNAs) were retrieved from three databases: TargetScan, miRBase and miRanda.Results:A total of 503 DEGs were obtained. Functional enrichment analysis showed that immune response, signaling pathways and apoptosis were significantly over-represented. Six key genes with big degree, betweenness and clustering coefficient were then revealed, which might play important roles in the development of IS. In addition, 57 differentially expressed miRNAs targeting the 6 genes were retrieved.Conclusions:Our study provides insights into the pathogenesis of IS and potential targets to treat the disease.

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Investigation and Functional Enrichment Analysis of the Human Host Interaction Network with Common Gram-Negative Respiratory Pathogens Predicts Possible Association with Lung Adenocarcinoma

Pathophysiology ◽

10.3390/pathophysiology28010003 ◽

2021 ◽

Vol 28 (1) ◽

pp. 20-33

Author(s):

Lydia-Eirini Giannakou ◽

Athanasios-Stefanos Giannopoulos ◽

Chrissi Hatzoglou ◽

Konstantinos I. Gourgoulianis ◽

Erasmia Rouka ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Cell Junctions ◽

Respiratory Pathogens ◽

Gram Negative ◽

Human Proteins ◽

Apoptotic Pathways

Haemophilus influenzae (Hi), Moraxella catarrhalis (MorCa) and Pseudomonas aeruginosa (Psa) are three of the most common gram-negative bacteria responsible for human respiratory diseases. In this study, we aimed to identify, using the functional enrichment analysis (FEA), the human gene interaction network with the aforementioned bacteria in order to elucidate the full spectrum of induced pathogenicity. The Human Pathogen Interaction Database (HPIDB 3.0) was used to identify the human proteins that interact with the three pathogens. FEA was performed via the ToppFun tool of the ToppGene Suite and the GeneCodis database so as to identify enriched gene ontologies (GO) of biological processes (BP), cellular components (CC) and diseases. In total, 11 human proteins were found to interact with the bacterial pathogens. FEA of BP GOs revealed associations with mitochondrial membrane permeability relative to apoptotic pathways. FEA of CC GOs revealed associations with focal adhesion, cell junctions and exosomes. The most significantly enriched annotations in diseases and pathways were lung adenocarcinoma and cell cycle, respectively. Our results suggest that the Hi, MorCa and Psa pathogens could be related to the pathogenesis and/or progression of lung adenocarcinoma via the targeting of the epithelial cellular junctions and the subsequent deregulation of the cell adhesion and apoptotic pathways. These hypotheses should be experimentally validated.

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Diagnostic model of combined ceRNA and DNA methylation related genes in esophageal carcinoma

PeerJ ◽

10.7717/peerj.8831 ◽

2020 ◽

Vol 8 ◽

pp. e8831 ◽

Cited By ~ 1

Author(s):

Xiaojiao Guan ◽

Yao Yao ◽

Guangyao Bao ◽

Yue Wang ◽

Aimeng Zhang ◽

...

Keyword(s):

Gene Expression ◽

Esophageal Cancer ◽

Esophageal Carcinoma ◽

Differentially Expressed Genes ◽

Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Diagnostic Model ◽

Link Type ◽

Key Genes

Esophageal cancer is a common malignant tumor in the world, and the aim of this study was to screen key genes related to the development of esophageal cancer using a variety of bioinformatics analysis tools and analyze their biological functions. The data of esophageal squamous cell carcinoma from the Gene Expression Omnibus (GEO) were selected as the research object, processed and analyzed to screen differentially expressed microRNAs (miRNAs) and differential methylation genes. The competing endogenous RNAs (ceRNAs) interaction network of differentially expressed genes was constructed by bioinformatics tools DAVID, String, and Cytoscape. Biofunctional enrichment analysis was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression of the screened genes and the survival of the patients were verified. By analyzing GSE59973 and GSE114110, we found three down-regulated and nine up-regulated miRNAs. The gene expression matrix of GSE120356 was calculated by Pearson correlation coefficient, and the 11696 pairs of ceRNA relation were determined. In the ceRNA network, 643 lncRNAs and 147 mRNAs showed methylation difference. Functional enrichment analysis showed that these differentially expressed genes were mainly concentrated in the FoxO signaling pathway and were involved in the corresponding cascade of calcineurin. By analyzing the clinical data in The Cancer Genome Atlas (TCGA) database, it was found that four lncRNAs had an important impact on the survival and prognosis of esophageal carcinoma patients. QRT-PCR was also conducted to identify the expression of the key lncRNAs (RNF217-AS1, HCP5, ZFPM2-AS1 and HCG22) in ESCC samples. The selected key genes can provide theoretical guidance for further research on the molecular mechanism of esophageal carcinoma and the screening of molecular markers.

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System Analysis of MIRNAs in Maize Internode Elongation

Biomolecules ◽

10.3390/biom9090417 ◽

2019 ◽

Vol 9 (9) ◽

pp. 417

Author(s):

Chuanxi Peng ◽

Xing Wang ◽

Tianyu Feng ◽

Rui He ◽

Mingcai Zhang ◽

...

Keyword(s):

Target Genes ◽

System Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Internode Elongation ◽

Differentially Expressed Mirnas ◽

Post Transcriptional Regulation

MicroRNAs (miRNAs), the post-transcriptional gene regulators, are known to play an important role in plant development. The identification of differentially expressed miRNAs could better help us understand the post-transcriptional regulation that occurs during maize internode elongation. Accordingly, we compared the expression of MIRNAs between fixed internode and elongation internode samples and classified six differentially expressed MIRNAs as internode elongation-responsive miRNAs including zma-MIR160c, zma-MIR164b, zma-MIR164c, zma-MIR168a, zma-MIR396f, and zma-MIR398b, which target mRNAs supported by transcriptome sequencing. Functional enrichment analysis for predictive target genes showed that these miRNAs were involved in the development of internode elongation by regulating the genes respond to hormone signaling. To further reveal how miRNA affects internode elongation by affecting target genes, the miRNA–mRNA–PPI (protein and protein interaction) network was constructed to summarize the interaction of miRNAs and these target genes. Our results indicate that miRNAs regulate internode elongation in maize by targeting genes related to cell expansion, cell wall synthesis, transcription, and regulatory factors.

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Comparative transcriptomic analysis of porcine peripheral blood reveals differentially expressed genes from the cytokine–cytokine receptor interaction pathway related to health status

Genome ◽

10.1139/gen-2017-0074 ◽

2017 ◽

Vol 60 (12) ◽

pp. 1021-1028 ◽

Cited By ~ 2

Author(s):

M.H. Ye ◽

H. Bao ◽

Y. Meng ◽

L.L. Guan ◽

P. Stothard ◽

...

Keyword(s):

Health Status ◽

Differentially Expressed Genes ◽

Peripheral Blood ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Cytokine Receptor ◽

Functional Enrichment ◽

Differentially Expressed ◽

Receptor Interaction ◽

Marker Genes

While some research has looked into the host genetic response in pigs challenged with specific viruses or bacteria, few studies have explored the expression changes of transcripts in the peripheral blood of sick pigs that may be infected with multiple pathogens on farms. In this study, the architecture of the peripheral blood transcriptome of 64 Duroc sired commercial pigs, including 18 healthy animals at entry to a growing facility (set as a control) and 23 pairs of samples from healthy and sick pen mates, was generated using RNA-Seq technology. In total, 246 differentially expressed genes were identified to be specific to the sick animals. Functional enrichment analysis for those genes revealed that the over-represented gene ontology terms for the biological processes category were exclusively immune activity related. The cytokine–cytokine receptor interaction pathway was significantly enriched. Nine functional genes from this pathway encoding members (as well as their receptors) of the interleukins, chemokines, tumor necrosis factors, colony stimulating factors, activins, and interferons exhibited significant transcriptional alteration in sick animals. Our results suggest a subset of novel marker genes that may be useful candidate genes in the evaluation and prediction of health status in pigs under commercial production conditions.

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Identification of novel genes and pathways in carotid atheroma using integrated bioinformatic methods

Scientific Reports ◽

10.1038/srep18764 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 10

Author(s):

Wenqing Nai ◽

Diane Threapleton ◽

Jingbo Lu ◽

Kewei Zhang ◽

Hongyuan Wu ◽

...

Keyword(s):

Signaling Pathway ◽

Transforming Growth Factor ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Transforming Growth Factor Β ◽

Functional Enrichment ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Atheromatous Plaques

Abstract Atherosclerosis is the primary cause of cardiovascular events and its molecular mechanism urgently needs to be clarified. In our study, atheromatous plaques (ATH) and macroscopically intact tissue (MIT) sampled from 32 patients were compared and an integrated series of bioinformatic microarray analyses were used to identify altered genes and pathways. Our work showed 816 genes were differentially expressed between ATH and MIT, including 443 that were up-regulated and 373 that were down-regulated in ATH tissues. GO functional-enrichment analysis for differentially expressed genes (DEGs) indicated that genes related to the “immune response” and “muscle contraction” were altered in ATHs. KEGG pathway-enrichment analysis showed that up-regulated DEGs were significantly enriched in the “FcεRI-mediated signaling pathway”, while down-regulated genes were significantly enriched in the “transforming growth factor-β signaling pathway”. Protein-protein interaction network and module analysis demonstrated that VAV1, SYK, LYN and PTPN6 may play critical roles in the network. Additionally, similar observations were seen in a validation study where SYK, LYN and PTPN6 were markedly elevated in ATH. All in all, identification of these genes and pathways not only provides new insights into the pathogenesis of atherosclerosis, but may also aid in the development of prognostic and therapeutic biomarkers for advanced atheroma.

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Comprehensive Analysis of Aquaporin Superfamily in Lung Adenocarcinoma

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.736367 ◽

2021 ◽

Vol 8 ◽

Author(s):

Guofu Lin ◽

Luyang Chen ◽

Lanlan Lin ◽

Hai Lin ◽

Zhifeng Guo ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Immune Cell ◽

Enrichment Analysis ◽

Tumor Infiltrating Lymphocytes ◽

Functional Enrichment Analysis ◽

Tumor Stage ◽

Stage I ◽

Functional Enrichment ◽

Gene Expressions ◽

Kaplan Meier

Background: Lung adenocarcinoma (LUAD) is the most predomintnt lung cancer subtype with increasing morbidity and mortality. Previous studies have shown that aquaporin (AQP) family genes were correlated with tumor progression and metastasis in several kinds of malignancies. However, their biological behaviors and prognostic values in LUAD have not been comprehensively elucidated.Methods: RNA sequencing and real-time reverse transcription PCR (RT-PCR) were used to assess AQP1/3/4/5 gene expressions in LUAD patients using GEPIA and UALCAN databases. And then Kaplan–Meier analysis, cBioPortal, Metascape, GeneMANIA, TISIDB, and TIMER were utilized to determine the prognostic value, mutation frequency, and immune cell infiltration of AQP family members in LUAD.Results: We found that AQP3 expression was significantly elevated and AQP1 expression was markedly reduced in LUAD patients, whereas the expression levels of AQP4 and AQP5 exhibited no significant changes. The Kaplan–Meier survival analysis indicated that the higher expressions of AQP1/4/5 were related to longer overall survival (OS). Of interest, AQP3 was significantly correlated with the clinical tumor stage and lower AQP3 expression showed favorable prognosis in stage I LUAD patients, which indicated that AQP3 may be a potential prognostic biomarker for patients. Through functional enrichment analysis, the functions of these four AQPs genes were mainly involved in the passive transport by aquaporins, water homeostasis, and protein tetramerization. Moreover, AQP1/3/4/5 expression was strongly associated with tumor-infiltrating lymphocytes (TILs) in LUAD.Conclusion: AQP3 can be used as a prognosis and survival biomarker for stage I LUAD. These findings may provide novel insights into developing molecular targeted therapies in LUAD.

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Meta-analysis of Transcriptomic Data Reveals Pathophysiological Modules Involved with Atrial Fibrillation

10.1101/2020.05.13.20100867 ◽

2020 ◽

Author(s):

Rodrigo Haas Bueno ◽

Mariana Recamonde-Mendoza

Keyword(s):

Atrial Fibrillation ◽

Differentially Expressed Genes ◽

Complex Disease ◽

Meta Analysis ◽

Differential Expression Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

P Value

Atrial fibrillation (AF) is a complex disease and affects millions of people around the world. The biological mechanisms that are involved with AF are complex and still need to be fully elucidated. Therefore, we performed a meta-analysis of transcriptome data related to AF to explore these mechanisms aiming at more sensitive and reliable results. Public transcriptomic datasets were downloaded, analyzed for quality control, and individually pre-processed. Differential expression analysis was carried out for each individual dataset, and the results were meta-analytically aggregated using the r-th ordered p-value method. We analyzed the final list of differentially expressed genes through network analysis, namely topological and modularity analysis, and functional enrichment analysis. The meta-analysis of transcriptomes resulted in 589 differentially expressed genes, whose protein-protein interaction network presented 11 hubs-bottlenecks and four main identified functional modules. These modules were enriched for, respectively, 23, 54, 33, and 53 biological pathways involved with the pathophysiology of AF, especially with the disease's structural and electrical remodeling processes. Stress of the endoplasmic reticulum, protein catabolism, oxidative stress, and inflammation are some of the enriched processes. Among hubs-bottlenecks genes, which are highly connected and probably have a key role in regulating these processes, we found HSPA5, ANK2, CTNNB1, and VWF. Further experimental investigation of our findings may shed light on the pathophysiology of the disease and contribute to the identification of new therapeutic targets and treatments.

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