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

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

Lung Cancer Management ◽

10.2217/lmt-2020-0009 ◽

2020 ◽

Vol 9 (2) ◽

pp. LMT30

Author(s):

Chuanli Ren ◽

Weixiu Sun ◽

Xu Lian ◽

Chongxu Han

Keyword(s):

Lung Adenocarcinoma ◽

Differentially Expressed Genes ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed ◽

Kaplan Meier ◽

Key Genes ◽

Core Genes

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 of Latent Diagnostic Biomarkers and Biological Pathways in Dermatomyositis Based on WGCNA

Journal of Oncology ◽

10.1155/2021/1920111 ◽

2021 ◽

Vol 2021 ◽

pp. 1-12

Author(s):

Shaxi Ouyang ◽

Yifang Liu ◽

Changjuan Xiao ◽

Qinghua Zeng ◽

Xun Luo ◽

...

Keyword(s):

Cell Lines ◽

Differentially Expressed Gene ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Receptor Interaction ◽

Interferon Α ◽

Pathway Enrichment Analysis ◽

Oligoadenylate Synthetase

Introduction. Dermatomyositis (DM) is a chronic autoimmune disease of predominantly lymphocytic infiltration mainly involving the transverse muscle. Its pathogenesis is remaining unknown. This research is designed to probe the latent pathogenesis of dermatomyositis, identify potential biomarkers, and reveal the pathogenesis of dermatomyositis through information biology analysis of gene chips. Methods. In this study, we utilised the GSE14287 and GSE11971 datasets rooted in the Gene Expression Omnibus (GEO) databank, which included a total of 62 DM samples and 9 normal samples. The datasets were combined, and the differentially expressed gene sets were subjected to weighted gene coexpression network analysis, and the hub gene was screened using a protein interaction network from genes in modules highly correlated with dermatomyositis progression. Results. A total of 3 key genes—myxovirus resistance-2 (MX2), oligoadenylate synthetase 1 (OAS1), and oligoadenylate synthetase 2 (OAS2)—were identified in combination with cell line samples, and the expressions of the 3 genes were verified separately. The results showed that MX2, OAS1, and OAS2 were highly expressed in LPS-treated cell lines compared to normal cell lines. The results of pathway enrichment analysis of the genes indicated that all 3 genes were enriched in the cytosolic DNA signalling and cytokine and cytokine receptor interaction signalling pathways; the results of functional enrichment analysis showed that all 3 were enriched in interferon-α response and interferon-γ response functions. Conclusions. This is important for the study of the pathogenesis and objective treatment of dermatomyositis and provides important reference information for the targeted therapy of dermatomyositis.

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Co-expression network analysis identifies specific hub genes in association with developmental neuronal remodeling in Drosophila melanogaster

10.7287/peerj.preprints.27586v1 ◽

2019 ◽

Author(s):

Yunze Liu ◽

Xiaojie Sun ◽

Aijun Qu

Keyword(s):

Drosophila Melanogaster ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Pathway Enrichment Analysis ◽

Hub Genes ◽

Protein Protein Interaction ◽

Neuronal Remodeling ◽

Gene Modules

As an evolutionarily conserved mechanism, developmental neuronal remodeling is needed for the proper wiring of the nervous system and is critical for understanding the neurodevelopment mechanisms. Previous studies have shown that during metamorphosis lots of Drosophila melanogaster mushroom body neurons experience stereotypic remodeling. However, the related regulators and downstream executors of pathways are yet unclear, especially studies of transcriptional gene co-expression analysis of nervous systems remain insufficient. In this study, we develop a weighted gene co-expression network (WGCNA) to classify gene modules associated with neuronal remodeling. Moreover, functional and pathway enrichment analysis with protein-protein network construction is applied to detect high informative hub genes in the targeted gene module. Thus, we select a total of five hub genes that play critical roles in neuronal remodeling and identify them with functional enrichment analysis and protein-protein interaction network. Overall, this study provides insight into the underlying molecular mechanism of developmental neuronal remodeling in Drosophila melanogaster.

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Co-expression network analysis identifies specific hub genes in association with developmental neuronal remodeling in Drosophila melanogaster

10.7287/peerj.preprints.27586 ◽

2019 ◽

Author(s):

Yunze Liu ◽

Xiaojie Sun ◽

Aijun Qu

Keyword(s):

Drosophila Melanogaster ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Pathway Enrichment Analysis ◽

Hub Genes ◽

Protein Protein Interaction ◽

Neuronal Remodeling ◽

Gene Modules

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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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Investigation of Key Genes associated with Prostate Cancer using RNA-Seq Data

The International Journal of Biological Markers ◽

10.5301/jbm.5000056 ◽

2014 ◽

Vol 29 (1) ◽

pp. e86-e92 ◽

Cited By ~ 1

Author(s):

Jitao Wu ◽

Fan Feng ◽

Diandong Yang ◽

Shengqiang Yu ◽

Jianqiu Liu ◽

...

Keyword(s):

Prostate Cancer ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment ◽

Normal Sample ◽

Pathway Enrichment Analysis ◽

Rna Seq ◽

Cancer Sample ◽

Key Genes

We aimed to identify key genes associated with prostate cancer using RNA-sequencing (RNA-seq) data. RNA-seq data, including 1 cancer sample and 1 adjacent normal sample, were downloaded from the NCBI SRA database and the differentially expressed genes (DEGs) were identified with the software Cufflinks. Functional enrichment analysis was performed to uncover the biological functions of DEGs. Regulatory information was retrieved from the IPA database and a network was established. A total of 147 DEGs were obtained, including 96 downregulated and 51 upregulated DEGs. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis suggested that metabolism and signal transduction were the 2 major functions that were significantly influenced. Moreover, an interaction network was built. In conclusion, a number of DEGs was identified and their roles in the pathogenesis of cancer were supported by previous studies. More studies are necessary to further validate their usefulness in the diagnosis and treatment of prostate cancer.

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CircRNA/lncRNA-miRNA-mRNA network in the blood exosomes of patients with atherosclerosis

10.21203/rs.3.rs-496464/v1 ◽

2021 ◽

Author(s):

Wan Zhang ◽

Ting Zhu ◽

Li Li ◽

Zhenyu Guo

Keyword(s):

Signaling Pathway ◽

Area Under The Curve ◽

Interaction Network ◽

Enrichment Analysis ◽

Arterial Disease ◽

Differentially Expressed ◽

Estrogen Signaling ◽

Pathway Enrichment Analysis ◽

Clinical Value ◽

Positive Regulation

Abstract Background: Atherosclerosis (AS) is a systemic, chronic and multifocal disease and is the primary pathological basis of cardiovascular diseases, such as coronary heart disease (CHD) and peripheral arterial disease (PAD). Our study attempted to identify aberrant exosome-derived circRNAs in AS and determine their potential clinical value. Methods: The expression of mRNA, circRNA and lncRNA in the blood exosomes of CHD patients and healthy controls was obtained from the exoRBase database. The corresponding miRNAs of mRNA, circRNA and lncRNA were predicted via ENCORI and the miRcode database. The circRNA/lncRNA-miRNA-mRNA interaction network was established based on a competitive endogenous RNA regulatory mechanism. Aberrant circRNAs in the aforementioned network were validated in patients with PAD by real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Results: Based on the cutoff criteria of P<0.05, we identified 85 differentially expressed circRNAs (4 up- and 81 downregulated), 43 differentially expressed lncRNAs (24 up- and 19 downregulated) and 312 differentially expressed genes (55 up- and 257 downregulated). Gene Ontology (GO) analysis revealed that the biological process (BP) terms of the DEGs were significantly enriched in the positive regulation of phosphoprotein phosphatase activity and the positive regulation of protein dephosphorylation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that DEGs were closely related to the glucagon signaling pathway and estrogen signaling pathway. The relative expression level of hsa_circ_0001360 was significantly downregulated in blood exosomes from patients with PAD, exhibiting an area under the curve of 0.92 (P=0.0283). Conclusion: The circRNA/lncRNA-miRNA-mRNA interaction network might help to elucidate the pathogenesis of AS. Hsa_circ_0001360 was significantly downregulated in blood exosomes in patients with PAD, and this RNA might represent an important diagnostic biomarker of AS.

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A comprehensive transcriptomic view on the role of SMAD4 gene by RNAi-mediated knockdown in porcine follicular granulosa cells

Reproduction ◽

10.1530/rep-16-0034 ◽

2016 ◽

Vol 152 (1) ◽

pp. 81-89 ◽

Cited By ~ 13

Author(s):

Lifan Zhang ◽

Xing Du ◽

Shengjuan Wei ◽

Dongfeng Li ◽

Qifa Li

Keyword(s):

Cell Cycle ◽

Signaling Pathway ◽

Granulosa Cells ◽

Transforming Growth Factor Beta ◽

Transforming Growth Factor ◽

Current Knowledge ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Functional Enrichment

As a key mediator of the transforming growth factor-beta (TGF-β) signaling pathway, which plays a pivotal role in regulating mammalian reproductive performance, Sma- and Mad-related protein 4 (SMAD4) is closely associated with the development of ovarian follicular. However, current knowledge of the genome-wide view on the role ofSMAD4gene in mammalian follicular granulosa cells (GCs) is still largely unknown. In the present study, RNA-Seq was performed to investigate the effects ofSMAD4knockdown by RNA interference (SMAD4-siRNA) in porcine follicular GCs. A total of 1025 differentially expressed genes (DEGs), including 530 upregulated genes and 495 downregulated genes, were identified inSMAD4-siRNA treated GCs compared with that treated with NC-siRNA. Furthermore, functional enrichment analysis indicated that upregulated DEGs inSMAD4-siRNA treated cells were mainly enriched in cell-cycle related processes, interferon signaling pathway, and immune system process, while downregulated DEGs inSMAD4-siRNA treated cells were mainly involved in extracellular matrix organization/disassembly, pathogenesis, and cell adhesion. In particular, cell cycle and TGF-β signaling pathway were discovered as the canonical pathways changed underSMAD4-silencing. Taken together, our data revealsSMAD4knockdown alters the expression of numerous genes involved in key biological processes of the development of follicular GCs and provides a novel global clue of the role ofSMAD4gene in porcine follicular GCs, thus improving our understanding of regulatory mechanisms ofSMAD4gene in follicular development.

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