scholarly journals Global transcriptome analysis to identify critical genes involved in the pathology of osteoarthritis

2018 ◽  
Vol 7 (4) ◽  
pp. 298-307 ◽  
Author(s):  
X. Zhang ◽  
Y. Bu ◽  
B. Zhu ◽  
Q. Zhao ◽  
Z. Lv ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Roc Analysis ◽  
Bioinformatics Analysis ◽  
Kegg Pathway ◽  
Diagnostic Value ◽  
Gene Expression Omnibus ◽  
Qrt Pcr ◽  
Global Transcriptome ◽  
Synovial Tissues ◽  
Pathway Analyses

Objectives The aim of this study was to identify key pathological genes in osteoarthritis (OA). Methods We searched and downloaded mRNA expression data from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) of joint synovial tissues from OA and normal individuals. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses were used to assess the function of identified DEGs. The protein-protein interaction (PPI) network and transcriptional factors (TFs) regulatory network were used to further explore the function of identified DEGs. The quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the result of bioinformatics analysis. Electronic validation was performed to verify the expression of selected DEGs. The diagnosis value of identified DEGs was accessed by receiver operating characteristic (ROC) analysis. Results A total of 1085 DEGs were identified. KEGG pathway analysis displayed that Wnt was a significantly enriched signalling pathway. Some hub genes with high interactions such as USP46, CPVL, FKBP5, FOSL2, GADD45B, PTGS1, and ZNF423 were identified in the PPI and TFs network. The results of qRT-PCR showed that GADD45B, ADAMTS1, and TFAM were down-regulated in joint synovial tissues of OA, which was consistent with the bioinformatics analysis. The expression levels of USP46, CPVL, FOSL2, and PTGS1 in electronic validation were compatible with the bio-informatics result. CPVL and TFAM had a potential diagnostic value for OA based on the ROC analysis. Conclusion The deregulated genes including USP46, CPVL, FKBP5, FOSL2, GADD45B, PTGS1, ZNF423, ADAMTS1, and TFAM might be involved in the pathology of OA. Cite this article: X. Zhang, Y. Bu, B. Zhu, Q. Zhao, Z. Lv, B. Li, J. Liu. Global transcriptome analysis to identify critical genes involved in the pathology of osteoarthritis. Bone Joint Res 2018;7:298–307. DOI: 10.1302/2046-3758.74.BJR-2017-0245.R1.

scholarly journals Bioinformatics Analysis and Identification of Genes and Pathways in Ischemic Cardiomyopathy

2021 ◽  
Author(s):  
Jing Cao ◽  
Zhaoya Liu ◽  
Jie Liu ◽  
Chan Li ◽  
Guogang Zhang ◽  
...  
Keyword(s):  
Network Analysis ◽  
Ischemic Cardiomyopathy ◽  
Bioinformatics Analysis ◽  
Kegg Pathway ◽  
Gene Expression Omnibus ◽  
Hub Genes ◽  
Ppi Networks ◽  
Regulated Expression ◽  
Limma Package ◽  
Pathway Analyses

Abstract BackgroundIschemic cardiomyopathy (ICM) is considered to be the common cause of heart failure, which has high prevalence and mortality. This study aimed to investigate the different expressed genes (DEGs) and pathways in the pathogenesis of ICM using bioinformatics analysis.MethodsThe control and ICM datasets GSE116250，GSE46224 and GSE5406 were collected from the gene expression omnibus (GEO) database. DEGs were identified using limma package of R software and co-expressed genes were identified with Venn diagrams. Then, the gene otology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explored the biological functions and signaling pathways. Protein-protein interaction (PPI) networks were assembled with Cytoscape software to identify hub genes related to the pathogenesis of ICM.ResultsA total of 844 DEGs were screened from GSE116250, of which 447 up-regulated and 397 down-regulated genes respectively. A total of 99 DEGs were singled out from GSE46224, of which 58 up-regulated and 41 down-regulated genes respectively. 30 DEGs were screened from GSE5406, including 10 genes with up-regulated expression and 20 genes with down-regulated expression. 5 up-regulated and 3 down-regulated co-expressed DEGs were intersected in three datasets. GO and KEGG pathway analyses revealed that DEGs mainly enriched in collagen fibril organization, protein digestion and absorption, AGE-RAGE signaling pathway and other related pathways. Collagen alpha-1(III) chain (COL3A1), collagen alpha-2(I) chain (COL1A2) and lumican (LUM) are the three hub genes in all three datasets through PPI network analysis. The expression of 5 DEGs (SERPINA3, FCN3, COL3A1, HBB, MXRA5) in heart tissues by qRT-PCR results were consistent with our GEO analysis, while expression of 3 DEGs (ASPN, LUM, COL1A2) were opposite with GEO analysis.ConclusionsThese findings from this bioinformatics network analysis investigated key hub genes, which contributed to better understand the mechanism and new therapeutic targets of ICM.

scholarly journals Screening Key Differentially Expressed Genes in Kawasaki Disease via Integrated Analysis

2021 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Keliang Li ◽  
Yan Jiao ◽  
Jingjing Liang ◽  
Pingping Pan ◽  
Yanji Zhu ◽  
...  
Keyword(s):  
Kawasaki Disease ◽  
Differentially Expressed Genes ◽  
Roc Analysis ◽  
Expression Patterns ◽  
Diagnostic Value ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Go Annotation ◽  
Qrt Pcr

Background: The current study was done to identify key genes associated with Kawasaki disease (KD). Methods: Three datasets were collected from Gene Expression Omnibus (GEO) database. Then, differentially expressed genes (DEGs) analysis, gene ontology (GO) annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to determine the expression levels of DEGs in KD. Receiver operating characteristic (ROC) analysis was performed to assess the diagnostic value of DEGs. Results: In total, 2923 DEGs (1239 up- and 1684 down-regulated genes) were detected in KD. Ribosome, Leishmaniasis, and Tuberculosis significantly enriched KEGG pathways of DEGs. Six DEGs, including ADM, S100A12, ZNF438, MYD88, FCGR2A, and FCGR3B, were selected for qRT-PCR validation. Except for MYD88, the qRT-PCR results displayed similar expression patterns with that in our integrated analysis. ROC analysis revealed the diagnostic value of the six DEGs. Conclusions: Our study was expected to provide clues toward understanding the pathophysiology of KD inflammation.

scholarly journals 975. Why Sex Make a Difference in HIV Clinical Course? Bioinformatics Analysis of Differential Expressed Gene in Females and Males with HIV Disease

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S516-S517
Author(s):  
Kulachanya Suwanwongse ◽  
Nehad Shabarek
Keyword(s):  
Gene Expression ◽  
Bioinformatics Analysis ◽  
Underlying Mechanism ◽  
Gene Expression Omnibus ◽  
Functional Enrichment ◽  
Gender Inequalities ◽  
Hiv Disease ◽  
Go Analysis ◽  
Hiv Progression ◽  
Pathway Analyses

Abstract Background Human immunodeficiency virus (HIV) disease progression are different among genders, in which women usually progress to acquired immunodeficiency syndrome (AIDS) faster than men. The mechanisms resulting in the gender biases of HIV progression are unclear. We conducted a bioinformatics analysis of differentially expressed genes (DEGs) in women and men with HIV disease to understand the sex-based differences in HIV pathogenesis. Methods We obtained microarray data from the Gene Expression Omnibus (GEO) database using our pre-defined search strategy and analyzed data using the GEO2R platform. The t-test was done to compare DEGs between females and males with HIV diseases. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was implemented to systematically extract biological features and processes of retrieving DEGs via gene ontology (GO) analysis. A Systemic search was performed to evaluate each DEG function and its possible association with HIV. Results One gene expression profiling data were retrieved: GSE 140713, composed of 40 males and 10 females with HIV1 infected samples. A GEO2R analysis yielded 19 DEGs (Table 1). The GO analysis result was demonstrated in Tables 2 and 3. Following a systemic search, we found two DEGs, which have previous studies reported an association with HIV: DDX3X (20 studies) and PDS5 (1 study). We proposed DDX3X (t 5.3, p 0.0037) is responsible for gender inequalities of HIV progression because of: 1. DDX3X is needed in the HIV1 life cycle. 2. Several studies confirmed a positive correlation between DDX3X expression and HIV1 replication. 3. Our study found an up-regulated DDX3X expression in women corresponded to the fact that women progress to AIDS faster than men. 4. Our GO analysis showed female up-regulated genes were enriched in positive regulation of the gene expression pathway, which can be explained by DDX3X and its underlying mechanism. Table 1: DEGs in women and men with HIV1 disease Table 2: GO functional enrichment pathway analyses of overall retrieving DEGs Table 3: GO functional enrichment pathway analyses of down- and up-regulated clusters of DEGs Conclusion Aberrant DDX3X expression may contribute to sex-based differences in HIV disease. Drugs modifying DDX3X gene expression will be beneficial in the treatment of HIV especially resolving the HIV drug resistance problem because current anti-HIV drugs target viral components posed the risk of viral mutation. Disclosures All Authors: No reported disclosures

scholarly journals MiR-210 has the capacity to serve as a diagnostic biomarker for laryngeal carcinoma patient

2020 ◽  
Author(s):  
Lili Wang ◽  
Hongguang Song ◽  
Shiming Yang
Keyword(s):  
Laryngeal Carcinoma ◽  
Clinical Characteristics ◽  
Roc Analysis ◽  
Diagnostic Value ◽  
Diagnostic Biomarker ◽  
Chi Square ◽  
Qrt Pcr ◽  
Elevated Expression ◽  
Chi Square Test ◽  
Auc Value

Abstract Background Early diagnosis represents a great challenge for laryngeal carcinoma patients. MiR-210 is involved in various human cancers. In this study, we aimed to investigate the diagnostic performance of serum miR-210 in laryngeal carcinoma. Methods In our study, qRT-PCR was performed to determine the serum miR-210 level in 137 laryngeal carcinoma patients and 79 healthy volunteers. The association of serum miR-210 level with clinical characteristics of the patients was estimated by chi-square test. ROC analysis was applied to evaluate the diagnostic value of miR-210 in laryngeal carcinoma. Results Serum miR-210 level was higher in laryngeal carcinoma patients than that in healthy group (P < 0.001). Moreover, its elevated expression was positively associated with TNM stage (P = 0.000) and distant metastasis (P = 0.001). The AUC value of the ROC curve was 0.893, suggesting the possibility of serum miR-210 as a diagnostic biomarker for the disease. The cut-off value was 4.685, with the sensitivity of 83.2% and the specificity of 84.8%. Conclusion MiR-210 serves as an oncogene in progression of laryngeal carcinoma. Serum miR-210 may be a potential diagnostic biomarker for laryngeal carcinoma.

scholarly journals Transcriptome Analysis of Aedes aegypti Aag2 Cells in Response to Dengue Virus-2 Infection

2020 ◽  
Author(s):  
Man-jin Li ◽  
Ce-jie Lan ◽  
He-ting Gao ◽  
Dan Xing ◽  
Zhen-yu Gu ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Dengue Virus ◽  
Cell Line ◽  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Bioinformatics Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Sequencing Data ◽  
Qrt Pcr

Abstract Background: Dengue virus (DENV) is a flavivirus transmitted by mosquitoes that is prevalent in tropical and subtropical countries and has four serotypes (DENV1-4). Aedes aegypti, as the main transmission vector of DENV, exhibits strong infectivity and transmission. With the aim of obtaining a better understanding of the Ae. aegypti-DENV interaction, the transcriptome changes in DENV-2-infected Aag2 cells were studied to describe the immune responses of mosquitoes using the Ae. aegypti Aag2 cell line as a model.Methods: RNAseq technology was used to sequence the transcripts of the Ae. aegypti Aag2 cell line before and after infection with DENV-2. A bioinformatics analysis was then performed to assess the biological functions of the differentially expressed genes, and the sequencing data were verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR).Results: The transcriptome analysis generated 8866 unigenes that were found in both groups, 225 unigenes that were only found in the infection group, and 683 unigenes that only existed in the control group. A total of 1199 differentially expressed genes, including 1014 upregulated and 185 downregulated genes, were identified. The bioinformatics analysis showed that the differentially expressed genes were mainly involved in the longevity regulating pathway, circadian rhythm, DNA replication, and peroxisome, purine, pyrimidine, and drug metabolism. The qRT-PCR verification results showed the same trend, which confirmed that the expression of the differentially expressed genes had changed and that the transcriptome sequencing data were reliable.Conclusions: This study investigated the changes in the transcriptome levels in the DENV-2-infected Ae. aegypti Aag2 cell line, which provides a faster and effective method for discovering genes related to Ae. aegypti pathogen susceptibility. The findings provide basic data and directions for further research on the complex mechanism underlying host-pathogen interactions.

scholarly journals Bioinformatics Analysis Identifying Key Biomarkers in Bladder Cancer

Data ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. 38
Author(s):  
Chuan Zhang ◽  
Mandy Berndt-Paetz ◽  
Jochen Neuhaus
Keyword(s):  
Bladder Cancer ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Kegg Pathway ◽  
Tumor Stage ◽  
Hub Genes ◽  
Go Enrichment ◽  
Comprehensive Information ◽  
Pathway Analyses ◽  
Potential Biomarkers

Our goal was to find new diagnostic and prognostic biomarkers in bladder cancer (BCa), and to predict molecular mechanisms and processes involved in BCa development and progression. Notably, the data collection is an inevitable step and time-consuming work. Furthermore, identification of the complementary results and considerable literature retrieval were requested. Here, we provide detailed information of the used datasets, the study design, and on data mining. We analyzed differentially expressed genes (DEGs) in the different datasets and the most important hub genes were retrieved. We report on the meta-data information of the population, such as gender, race, tumor stage, and the expression levels of the hub genes. We include comprehensive information about the gene ontology (GO) enrichment analyses and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. We also retrieved information about the up- and down-regulation of genes. All in all, the presented datasets can be used to evaluate potential biomarkers and to predict the performance of different preclinical biomarkers in BCa.

scholarly journals Bioinformatics Analysis IdentifiesThrombospondin-1 and its related micro RNAs as biomarkers for Hepatocellular carcinoma

2020 ◽  
Author(s):  
Wei xuan ◽  
Dandan Song ◽  
Yunjia Ren ◽  
Ming Li
Keyword(s):  
Hepatocellular Carcinoma ◽  
Predictive Power ◽  
Bioinformatics Analysis ◽  
Diagnostic Value ◽  
Secretory Protein ◽  
Gene Expression Omnibus ◽  
Public Access ◽  
Transcriptome Data ◽  
Micro Rnas ◽  
And Control

Abstract Hepatocellular carcinoma (HCC) has a poor prognosis, while the diagnosis biomarkers or treatment targets for HCC are still lacking. Recently, mining strategies on public access databases has been successfully used to discover novel and sensitive biomarkers. In this study, bioinformatics analysis of the genomic and transcriptome data of HCC PBMC samples obtained from the Gene Expression Omnibus datasets. The analysis results showed that thrombospondin-1 (THBS-1) was dysregulated in HCC, and might be as biomarkers as it is a secretory protein and found to participate in liver dysfunction including HCC development. THBS-1 related micro RNAs are identified by bioinformatics analysis and tested as biomarkers as they are altered in many tumors and stable in circulation. The results showed that plasma THBS-1 and miR-194 were down-regulated in HCC patients and their correlations were positive. Whereas plasma level of miR-338-3p was significantly increased in the HCC patients and negatively correlated with THBS-1 and they showed a highly significant diagnostic value in discriminating HCC. In addition, THBS-1 and miR-338-3p combination displayed higher predictive power than them alone, and addition of miR-338-3p might enhance predictive power of AFP for HCC. Our data showed that THBS-1 and miR-338-3p displayed a highly significant diagnostic value in discriminating between HCC patients and control subjects. Addition of miR-338-3p might enhance the predictive potency of AFP for HCC.

scholarly journals CircRNA circ_0075796 is downregulated in breast cancer and suppresses cell proliferation, migration and invasion

2021 ◽  
Author(s):  
Yao Xu ◽  
Ya-Wen Wang ◽  
Xu Chen ◽  
Can Liu ◽  
Yan-Duo Chen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Proliferation ◽  
Bioinformatics Analysis ◽  
Diagnostic Value ◽  
Migration And Invasion ◽  
Normal Tissues ◽  
Qrt Pcr ◽  
Cancer Tissues ◽  
Normal Controls

Abstract Background Emerging evidence shows that circular RNAs (circRNAs) play crucial parts in tumorigenesis and progression. In this work, the expression, clinical significance, function and potential mechanism of circ_0075796 in breast cancer were explored. Methods The expression of circ_0075796 in 189 pairs of breast cancer tissues and adjacent normal tissues was detected by quantitative real-time PCR (qRT-PCR). Cell Counting Kit-8 (CCK-8) assay, methyl thiazolyl tetrazolium (MTT) assay and colony formation assay were conducted for cell proliferation. Transwell assay and wound healing assay were used for cell migration and invasion. Flow cytometry analysis was adopted for cell cycle and cell apoptosis. The cellular localization of circ_0075796 was determined by fluorescence in situ hybridization (FISH). The circ_0075796/miR-452-3p/SAMD5 axis was screened out by bioinformatics analysis and verified by qRT-PCR. Methylated RNA Immunoprecipitation (MeRIP) was used to detect the N6-methyladenosine (m6A) modification levels of circ_0075796. QRT-PCR was used to detect the expression of RNA binding protein Quaking (QKI) in breast cancer tissues and adjacent normal tissues. Results circ_0075796 was downregulated in breast cancer tissues compared with adjacent normal tissues. In addition, circ_0075796 showed satisfactory diagnostic value to discriminate breast cancer and normal controls. Downregulated circ_0075796 expression was correlated with lymph node metastasis, HER2 expression, larger tumor size, high Ki-67 expression, advanced histological grade, aggressive molecular subtypes and advanced clinical stages. Overexpression of circ_0075796 inhibited cell proliferation, migration and invasion in vitro. FISH showed that circ_0075796 was localized in the cytoplasm and nucleus of breast cancer cells. Bioinformatics analysis and qRT-PCR revealed the potential circ_0075796/miR-452-3p/SAMD5 axis. Moreover, circ_0075796 showed lower m6A modification levels in breast cancer tissues compared to adjacent normal tissues. QKI was predicted to contain binding sites of circ_0075796 and was downregulated in breast cancer tissues compared to adjacent normal controls. Conclusions circ_0075796 was downregulated in breast cancer compared to normal controls, and showed potential diagnostic value for breast cancer. Downregulation of circ_0075796 was correlated with aggressive clinical features of breast cancer and overexpression of circ_0075796 inhibited the progression of breast cancer in vitro, indicating that circ_0075796 may be related to tumorigenesis and development of breast cancer.

scholarly journals The long non-coding RNA landscape of periodontal ligament stem cells subjected to compressive force

2018 ◽  
Vol 41 (4) ◽  
pp. 333-342 ◽  
Author(s):  
Yiping Huang ◽  
Yingying Zhang ◽  
Xiaobei Li ◽  
Hao Liu ◽  
Qiaolin Yang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Compressive Stress ◽  
Periodontal Ligament ◽  
Kegg Pathway ◽  
Compressive Force ◽  
Differentially Expressed ◽  
Periodontal Ligament Stem Cells ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Pathway Analyses

Summary Objective The role of long non-coding ribonucleic acids (lncRNAs) during orthodontic tooth movement remains unclear. We explored the lncRNA landscape of periodontal ligament stem cells (PDLSCs) subjected to compressive force. Materials and methods PDLSCs were subjected to static compressive stress (2 g/cm2) for 12 hours. Total RNA was then extracted and sequenced to measure changes in lncRNA and messenger RNA (mRNA) expression levels. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the expression levels of certain lncRNAs. Differential expression analysis as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also performed. Results In total, 90 lncRNAs and 519 mRNAs were differentially expressed in PDLSCs under compressive stress. Of the lncRNAs, 72 were upregulated and 18 downregulated. The levels of eight lncRNAs of interest (FER1L4, HIF1A-AS2, MIAT, NEAT1, ADAMTS9-AS2, LUCAT1, MIR31HG, and DHFRP1) were measured via qRT-PCR, and the results were found to be consistent with those of RNA sequencing. GO and KEGG pathway analyses showed that a wide range of biological functions were expressed during compressive loading; most differentially expressed genes were involved in extracellular matrix organization, collagen fibril organization, and the cellular response to hypoxia. Conclusions The lncRNA expression profile was significantly altered in PDLSCs subjected to compressive stress. These findings expand our understanding of molecular regulation in the mechanoresponse of PDLSCs.

scholarly journals Identification of key genes in allergic rhinitis by bioinformatics analysis

2021 ◽  
Vol 49 (7) ◽  
pp. 030006052110295
Author(s):  
Yunfei Zhang ◽  
Yue Huang ◽  
Wen-xia Chen ◽  
Zheng-min Xu
Keyword(s):  
Allergic Rhinitis ◽  
Antigen Processing ◽  
Bioinformatics Analysis ◽  
Kegg Pathway ◽  
Validation Dataset ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Pathway Analyses ◽  
Antigen Processing And Presentation

Objective This study aimed to explore the potential molecular mechanism of allergic rhinitis (AR) and identify gene signatures by analyzing microarray data using bioinformatics methods. Methods The dataset GSE19187 was used to screen differentially expressed genes (DEGs) between samples from patients with AR and healthy controls. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were applied for the DEGs. Subsequently, a protein–protein interaction (PPI) network was constructed to identify hub genes. GSE44037 and GSE43523 datasets were screened to validate critical genes. Results A total of 156 DEGs were identified. GO analysis verified that the DEGs were enriched in antigen processing and presentation, the immune response, and antigen binding. KEGG analysis demonstrated that the DEGs were enriched in Staphylococcus aureus infection, rheumatoid arthritis, and allograft rejection. PPI network and module analysis predicted seven hub genes, of which six ( CD44, HLA-DPA1, HLA-DRB1, HLA-DRB5, MUC5B, and CD274) were identified in the validation dataset. Conclusions Our findings suggest that hub genes play important roles in the development of AR.

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