Identification of critical genes and pathways involved in intervertebral disc degeneration (IDD) An integrated bioinformatics analysis

2020 ◽  
Author(s):  
Jingyang Zhou ◽  
Feng Xin ◽  
Chuyu Xiao ◽  
Wuyuan Zhou
Keyword(s):  
Daily Life ◽  
Vital Role ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Diagnosis And Prognosis ◽  
Study Results ◽  
Validation Experiment ◽  
The One

Abstract Background: In western countries and China, back and neck pain has become a common problem that bothers daily life and severely influences the quality of our daily life. Among all factors that lead to chronic neck and back pain, IDD is the one that couldn’t be easily neglected. Methods: This study aims to figure out the critical genes and pathways involved in the development of IDD and provide a new aspect of following investigations on the etiology of IDD. We firstly systemically searched the GEO database and identified the differentially expressed genes (DEGs) from the expression profile dataset we selected. We secondly constructed the protein-protein interaction (PPI) network for DEGs, identified the top ten hub genes from the whole PPI network and found two statically and medically significant modules from the network, we then performed the GO and KEGG analysis on the DEGs, top ten hub genes, the PPI network and the two statically and medically modules. In the end, we provided the primers of the mRNAs of all DEGs, which will be useful for the validation experiment of this study. Results: FN1, MMP2, POSTN, COL3A1, TIMP3, FBN1, GJA1, TGFBI, EFEMP1 and ID1 were top ten hub genes identified from this study, and they may play a vital role in the development of IDD. Angiogenesis and integrin binging are crucial biological process and molecular function defined in this study, which are worthy of being intensely investigated.Conclusion: More studies on the top ten hub genes, the role of angiogenesis and integrin binding in IDD are urgently needed, which will benefit the prevention, screening, diagnosis and prognosis of IDD.

scholarly journals Overexpression of SKA Complex Is Associated With Poor Prognosis in Gliomas

2022 ◽  
Vol 12 ◽  
Author(s):  
Shoukai Yu
Keyword(s):  
Chromosome Segregation ◽  
Poor Prognosis ◽  
Nuclear Division ◽  
Prognostic Significance ◽  
Mrna Levels ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Spindle Microtubules

The spindle and kinetochore-associated complex is composed of three members: SKA1, SKA2, and SKA3. It is necessary for stabilizing spindle microtubules attaching to kinetochore (KT) in the middle stage of mitosis. The SKA complex is associated with poor prognosis in several human cancers. However, the role of SKA complex in rare malignant diseases, such as gliomas, has not been fully investigated. We investigated several databases, including Oncomine, UALCAN, and cBioPortal to explore the expression profile and prognostic significance of SKA complex in patients with gliomas. Gene ontology and Kyoto Encyclopedia of Genes and Genome pathways were used to analyze the potential enriched pathways. The genes co-expressed with SKA complex were identified and used for developing a protein-protein interaction (PPI) network using the STRING database. We found a significant overexpression of the mRNA levels of SKA1, SKA2, and SKA3 in patients with glioma patients. Higher expression of SKA1 and SKA3, but not SKA2, was significantly correlated with shorter overall survival of patients with glioma. In glioma, SKA complex was found to be involved in nuclear division, chromosome segregation, and DNA replication. The results of PPI network identified 10 hub genes (CCNB2, UBE2C, BUB1B, TPX2, CCNA2, CCNB1, MELK, TOP2A, PBK, and KIF11), all of which were overexpressed and negatively associated with prognosis of patients with glioma. In conclusion, our study sheds new insights into the biological role and prognostic significance of SKA complex in glioma.

The role of iron homeostasis in adipocyte metabolism

2021 ◽  
Author(s):  
Wan Ma ◽  
Li Jia ◽  
Qingqing Xiong ◽  
Yunfei Feng ◽  
Huahua Du
Keyword(s):  
Adipose Tissue ◽  
Energy Supply ◽  
Iron Homeostasis ◽  
Vital Role ◽  
Physiological Functions ◽  
The One

Iron plays a vital role in the metabolism of adipose tissue. On the one hand, iron is essential for differentiation, endocrine, energy supply and other physiological functions of adipocyte. Iron...

scholarly journals Differential Expression of mRNAs in Peripheral Blood Related to Prodrome and Progression of Alzheimer’s Disease

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Weishuang Xue ◽  
Jinwei Li ◽  
Kailei Fu ◽  
Weiyu Teng
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Peripheral Blood ◽  
Bioinformatics Analysis ◽  
Gene Expression Omnibus ◽  
Venn Diagram ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Ppi Networks

Alzheimer’s disease (AD) is a chronic progressive neurodegenerative disease that affects the quality of life of elderly individuals, while the pathogenesis of AD is still unclear. Based on the bioinformatics analysis of differentially expressed genes (DEGs) in peripheral blood samples, we investigated genes related to mild cognitive impairment (MCI), AD, and late-stage AD that might be used for predicting the conversions. Methods. We obtained the DEGs in MCI, AD, and advanced AD patients from the Gene Expression Omnibus (GEO) database. A Venn diagram was used to identify the intersecting genes. Gene Ontology (GO) and Kyoto Gene and Genomic Encyclopedia (KEGG) were used to analyze the functions and pathways of the intersecting genes. Protein-protein interaction (PPI) networks were constructed to visualize the network of the proteins coded by the related genes. Hub genes were selected based on the PPI network. Results. Bioinformatics analysis indicated that there were 61 DEGs in both the MCI and AD groups and 27 the same DEGs among the three groups. Using GO and KEGG analyses, we found that these genes were related to the function of mitochondria and ribosome. Hub genes were determined by bioinformatics software based on the PPI network. Conclusions. Mitochondrial and ribosomal dysfunction in peripheral blood may be early signs in AD patients and related to the disease progression. The identified hub genes may provide the possibility for predicting AD progression or be the possible targets for treatments.

The Screening and Identification of Key Biomarkers in Adrenocortical Carcinoma: Evidence from a Bioinformatics Analysis

2022 ◽  
Vol 12 (3) ◽  
pp. 523-532
Author(s):  
Xin Yan ◽  
Chunfeng Liang ◽  
Xinghuan Liang ◽  
Li Li ◽  
Zhenxing Huang ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Gene Ontology ◽  
Protein Interaction ◽  
Adrenocortical Carcinoma ◽  
Gene Expression Omnibus ◽  
Heparin Binding ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Upregulated Genes

<sec> <title>Objective:</title> This study aimed to identify the potential key genes associated with the progression and prognosis of adrenocortical carcinoma (ACC). </sec> <sec> <title>Methods:</title> Differentially expressed genes (DEGs) in ACC cells and normal adrenocortical cells were assessed by microarray from the Gene Expression Omnibus database. The biological functions of the classified DEGs were examined by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses and a protein–protein interaction (PPI) network was mapped using Cytoscape software. MCODE software was also used for the module analysis and then 4 algorithms of cytohubba software were used to screen hub genes. The overall survival (OS) examination of the hub genes was then performed by the ualcan online tool. </sec> <sec> <title>Results:</title> Two GSEs (GSE12368, GSE33371) were downloaded from GEO including 18 and 43 cases, respectively. One hundred and sixty-nine DEGs were identified, including 57 upregulated genes and 112 downregulated genes. The Gene Ontology (GO) analyses showed that the upregulated genes were significantly enriched in the mitotic cytokines is, nucleus and ATP binding, while the downregulated genes were involved in the positive regulation of cardiac muscle contraction, extracellular space, and heparin-binding (P < 0.05). The Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) pathway examination showed significant pathways including the cell cycle and the complement and coagulation cascades. The protein– protein interaction (PPI) network consisted of 162 nodes and 847 edges, including mitotic nuclear division, cytoplasmic, protein kinase binding, and cell cycle. All 4 identified hub genes (FOXM1, UBE2C, KIF11, and NDC80) were associated with the prognosis of adrenocortical carcinoma (ACC) by survival analysis. </sec> <sec> <title>Conclusions:</title> The present study offered insights into the molecular mechanism of adrenocortical carcinoma (ACC) that may be beneficial in further analyses. </sec>

scholarly journals The Role of Sufistic-Based Kiai Leadership in Developing the Character of Santri in the Pesantren

2021 ◽  
Vol 13 (3) ◽  
pp. 1705-1714
Author(s):  
Chusnul Muali ◽  
Moh Rofiki ◽  
Hasan Baharun ◽  
Zamroni Zamroni ◽  
Lukman Sholeh
Keyword(s):  
Essential Role ◽  
Vital Role ◽  
Qualitative Approach ◽  
Reduction Techniques ◽  
Study Results ◽  
Technological Developments ◽  
The Subject ◽  
Common Understanding

This study aims to describe Sufistic-based Kiai leadership's role in shaping Santri character at the Pesantren Nurul Jadid Paiton Probolinggo. This research is a case study qualitative approach, with Kiai as the subject. We collected data using interview, documentation, and observation techniques, then analyzed using reduction techniques, presenting data, and drawing conclusions. The results showed that the Sufistic-based Kiai's leadership had an essential role in fostering the character of the Santri. The study results indicate that the Sufistic-based Kiai leadership has a vital role in promoting the surface of the Santri. Kiai is a person who gives influence in building character with Uswah (Modelling). This study also found that the factors that influence low morale are that Santri has a common understanding of the latest technological developments. In Sufistic-based leadership, there are four things that a leader must possess: 1) The Tawasuth, 2) The nature of I'tidal, 3) The Tawazun, and 4) The Tasamuh.

scholarly journals The role of exosomal lncRNAs in cancer biology and clinical management

2021 ◽  
Author(s):  
Wuwen Zhang ◽  
Qinshi Wang ◽  
Yi Yang ◽  
Siyuan Zhou ◽  
Ping Zhang ◽  
...  
Keyword(s):  
Clinical Management ◽  
Cancer Biology ◽  
Cell Communication ◽  
Noncoding Rnas ◽  
Vital Role ◽  
Cancer Development ◽  
Cancer Cell Proliferation ◽  
Diagnosis And Prognosis ◽  
Multiple Processes

AbstractExosomes play a vital role in cell–cell communication within the cancer microenvironment. Exosomal long noncoding RNAs (lncRNAs) are important regulators in cancer development and are involved in multiple processes, including cancer cell proliferation, angiogenesis, metastasis, drug resistance, and immunomodulation. Changes in the levels of exosomal lncRNAs often appear with the occurrence and development of cancer. Therefore, exosomal lncRNAs can be used as biomarkers for cancer diagnosis and prognosis. Exosomal lncRNAs can also indicate the treatment response of patients receiving chemotherapy. Moreover, exosomal lncRNAs are potential therapeutic targets for cancer treatment. In this review, we summarize the role of exosomal lncRNAs in cancer biology as well as in clinical management. A more comprehensive and in-depth understanding of the role of exosomal lncRNAs in cancer may help us better understand the mechanism of cancer development and clinically manage cancer patients.

scholarly journals Weighted gene co-expression network analysis to define pivotal modules and genes in diabetic heart failure

2020 ◽  
Vol 40 (7) ◽  
Author(s):  
Weiwei Liang ◽  
FangFang Sun
Keyword(s):  
Heart Failure ◽  
Kegg Pathway ◽  
Diabetic Heart ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Light Yellow ◽  
Go Enrichment ◽  
Key Genes ◽  
Functional Analyses

Abstract This research was carried out to reveal specific hub genes involved in diabetic heart failure, as well as remarkable pathways that hub genes locate. The GSE26887 dataset from the GEO website was downloaded. The gene co-expression network was generated and central modules were analyzed to identify key genes using the WGCNA method. Functional analyses were conducted on genes of the clinical interest modules via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene ontology (GO) enrichment, associated with protein–protein interaction (PPI) network construction in a sequence. Centrality parameters of the PPI network were determined using the CentiScape plugin in Cytoscape. Key genes, defined as genes in the ≥95% percentile of the degree distribution of significantly perturbed networks, were identified. Twenty gene co-expression modules were detected by WGCNA analysis. The module marked in light yellow exhibited the most significant association with diabetes (P=0.08). Genes involved in this module were primarily located in immune response, plasma membrane and receptor binding, as shown by the GO analysis. These genes were primarily assembled in endocytosis and phagosomes for KEGG pathway enrichment. Three key genes, STK39, HLA-DPB1 and RAB5C, which may be key genes for diabetic heart failure, were identified. To our knowledge, our study is the first to have constructed the co-expression network involved in diabetic heart failure using the WGCNA method. The results of the present study have provided better understanding the molecular mechanism of diabetic heart failure.

scholarly journals Integrated WGCNA and PPI Network to Screen Hub Genes Signatures for Infantile Hemangioma

2021 ◽  
Vol 11 ◽  
Author(s):  
Miao Xu ◽  
Tianxiang Ouyang ◽  
Kaiyang Lv ◽  
Xiaorong Ma
Keyword(s):  
Differential Expression ◽  
Enrichment Analysis ◽  
Infantile Hemangioma ◽  
Ppi Network ◽  
Hub Genes ◽  
Protein Protein Interaction ◽  
Normal Tissues ◽  
Network Analyses ◽  
Cycle Arrest ◽  
Auc Value

BackgroundInfantile hemangioma (IH) is characterized by proliferation and regression.MethodsBased on the GSE127487 dataset, the differentially expressed genes (DEGs) between 6, 12, or 24 months and normal samples were screened, respectively. STEM software was used to screen the continued up-regulated or down-regulated in common genes. The modules were assessed by weighted gene co-expression network analysis (WGCNA). The enrichment analysis was performed to identified the biological function of important module genes. The area under curve (AUC) value and protein-protein interaction (PPI) network were used to identify hub genes. The differential expression of hub genes in IH and normal tissues was detected by qPCR.ResultsThere were 5,785, 4,712, and 2,149 DEGs between 6, 12, and 24 months and normal tissues. We found 1,218 DEGs were up-regulated or down-regulated expression simultaneously in common genes. They were identified as 10 co-expression modules. Module 3 and module 4 were positively or negatively correlated with the development of IH, respectively. These two module genes were significantly involved in immunity, cell cycle arrest and mTOR signaling pathway. The two module genes with AUC greater than 0.8 at different stages of IH were put into PPI network, and five genes with the highest degree were identified as hub genes. The differential expression of these genes was also verified by qRTPCR.ConclusionFive hub genes may distinguish for proliferative and regressive IH lesions. The WGCNA and PPI network analyses may help to clarify the molecular mechanism of IH at different stages.

scholarly journals Bioinformatics Approach to Identify Common Gene Signatures of Patients With Coronavirus 2019 and Lung Adenocarcinoma

2021 ◽  
Author(s):  
Xiao Liang ◽  
Yali Chen ◽  
Yuchao Fan
Keyword(s):  
Lung Adenocarcinoma ◽  
Severe Disease ◽  
Enrichment Analysis ◽  
Immune Checkpoints ◽  
Specific Gene ◽  
Ppi Network ◽  
Hub Genes ◽  
Immune Infiltration ◽  
Protein Protein Interaction ◽  
Tf Gene

Abstract Coronavirus disease 2019 (COVID-19) continues as a global pandemic. Patients with lung cancer infected with COVID-19 may develop severe disease or die. Treating such patients severely burdens overwhelmed healthcare systems. Here we identified potential pathological mechanisms shared between patients with COVID-19 and lung adenocarcinoma (LUAD). Co-expressed, differentially expressed genes (DEGs) in patients with COVID-19 and LUAD were identified and used to construct a protein-protein interaction (PPI) network and to perform enrichment analysis. We used the NetworkAnalyst platform to establish a co-regulatory of the co-expressed DEGs, and we used Spearman’s correlation to evaluate the significance of associations of hub genes with immune infiltration and immune checkpoints. Analysis of three datasets identified 112 shared DEGs, which were used to construct a protein-PPI network. Subsequent enrichment analysis revealed co-expressed genes related to biological process (BP), molecular function (MF), cellular component (CC) as well as to pathways, specific organs, cells and diseases. Ten co-expressed hub genes were employed to construct a gene-miRNA, transcription factor (TF)-gene and TF-miRNA network. Hub genes were significantly associated with immune infiltration and immune checkpoints. Finally methylation level of hub genes in LUAD was obtained via UALCAN database. The present multi-dimensional study reveals commonality in specific gene expression by patients with COVID-19 and LUAD. These findings provide insights into developing strategies for optimising the management and treatment of patients with LUAD with COVID-19.

scholarly journals Riding the Wave: Daily Life and Religion among Brazilian Immigrants to Japan in the Age of COVID-19 Pandemic

Religions ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 943
Author(s):  
Hugo Córdova Quero ◽  
Nilta Dias
Keyword(s):  
Daily Life ◽  
Faith Communities ◽  
Religious Institutions ◽  
Immigration Control ◽  
The World ◽  
Foreign Land ◽  
Areas Of Concern ◽  
Brazilian Immigrants ◽  
The One

In March 2020, the world folded before an imminent pandemic. Community gatherings, events, and rituals quickly moved online. Jobs halted or were conducted remotely. The fear of the COVID-19 pandemic impacted different areas of daily life. In this article, we propose examining and analyzing the experiences and narratives of Brazilian migrants in Japan. With the Immigration Control and Refugee Recognition Act amendment on 8 December 1989, thousands of Japanese descendants born and raised in the Americas migrated to Japan. They are the offspring of Japanese immigrants who established colonies in the Americas in the late nineteenth and early twentieth century. Over time, the community of Brazilian immigrants in Japan fluctuated from being a minority to become the fifth-largest ethnic group of immigrants. Our analysis focuses on two areas of concern in times of the COVID-19 pandemic: daily life—including gender, and religion. On the one hand, daily life became cumbersome due to issues related to language and the hardships of accessing health services in a foreign land. On the other hand, we state that in the process of adaptation to the new society, the role of faith communities has been notable in offering support to these immigrants. Religious institutions, in particular, confronted the fact of moving their support and activities online with the consequent difficulties for those who are not tech-savvy or lack reliable connectivity. Both situations impacted Brazilian immigrants in different ways during the COVID-19 pandemic and highlighted the agency they displayed in coping with its consequences.

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