Genetics research最新文献

{"title":"Epigenetic Application of ATAC-Seq Based on Tn5 Transposase Purification Technology.","authors":"Wangchun Li,&nbsp;U Tim Wu,&nbsp;Yu Cheng,&nbsp;Yanhao Huang,&nbsp;Lipeng Mao,&nbsp;Menghan Sun,&nbsp;Congling Qiu,&nbsp;Lin Zhou,&nbsp;Lijuan Gao","doi":"10.1155/2022/8429207","DOIUrl":"https://doi.org/10.1155/2022/8429207","url":null,"abstract":"<p><strong>Background: </strong>Assays of transposase accessible chromatin sequencing (ATAC-seq) is an efficient assay to investigate chromatin accessibility, which depends on the activity of a robust Tn5 transposase to fragment the genome while cutting in the sequencing adapters.</p><p><strong>Methods: </strong>We propose reliable approaches for purifying hyperactive Tn5 transposase by chitin magnetic bead sorting. Double-stranded DNA of J76 cells and 293T cells were digested and subjected to tagmentation as test samples with Tn5 transposase, and libraries were established and sequenced. Sequencing data was then analyzed for peak calling, GO enrichment, and motif analysis.</p><p><strong>Results: </strong>We report a set of rapid, efficient, and low-cost methods for ATAC-seq library construction and data analysis, through large-scale and rapid sequencing. These methods can provide a reference for the study of epigenetic regulation of gene expression.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":"8429207"},"PeriodicalIF":1.5,"publicationDate":"2022-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9388308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40350774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive Analysis on the Specific Role and Function of Mitochondrial Inner Membrane Protein MPV17 in Liver Hepatocellular Carcinoma.","authors":"Hanchuan Tao,&nbsp;Cheng Wang,&nbsp;Chongmei Lu,&nbsp;Ning Ma,&nbsp;Yifan Zhu,&nbsp;Shihai Xuan,&nbsp;Xiaojun Zhou","doi":"10.1155/2022/7236823","DOIUrl":"https://doi.org/10.1155/2022/7236823","url":null,"abstract":"<p><strong>Background: </strong>Liver hepatocellular carcinoma (LIHC) is the predominant type of liver cancer, and its treatment still faces great challenges presently. Mitochondrial inner membrane protein MPV17 is reported to be involved in multiple biological activities of cancers. Here, we seek to investigate the specific role and functions of MPV17 in LIHC progression.</p><p><strong>Methods: </strong>Firstly, MPV17 expressions in various tumors and corresponding normal samples and LIHC groups with various clinical features were analyzed, respectively. Next, the relationship between MPV17 expression and LIHC survival was analyzed and verified by AUC curves. Besides, differentially expressed genes (DEGs) for LIHC were screened from TCGA and then analyzed by GO and KEGG. Then, MPV17 was analyzed by prognostic model, Cox analysis, predictive nomogram, pathway correlation, and immunoassay. Finally, the functions of MPV17 were determined by CCK-8 and Tranwell assays.</p><p><strong>Results: </strong>In most tumors, MPV17 expression was higher than that in the normal group, and it was related to LIHC clinical features. In the LIHC survival analysis, highly expressed MPV17 was associated with a poor prognosis. Besides, 314 upregulated and 193 downregulated DEGs are mainly involved in the TNF signaling pathway and tyrosine metabolism. Through prognostic model, Cox analysis, and predictive nomogram, MPV17 had the prognostic value for LIHC. Gene-pathway correlation analysis showed that MPV17 had the strongest correlation with the G2M_checkpoint pathway. In an immunoassay, MPV17 had a strong correlation with many immune cells. Functional assays showed that MPV17 reduction in LIHC cells could inhibit cell invasion, migration, and proliferation.</p><p><strong>Conclusion: </strong>MPV17, as a tumor promoter, could be a new biomarker for LIHC diagnosis and prognosis and probably shed new light on the exploration of LIHC therapies.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":"7236823"},"PeriodicalIF":1.5,"publicationDate":"2022-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9325347/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40595593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome Classification Reveals Molecular Subgroups in Idiopathic Pulmonary Fibrosis.","authors":"Yuxia Liu,&nbsp;Chang Xu,&nbsp;Wenxin Gao,&nbsp;Huaqiong Liu,&nbsp;Chenglong Li,&nbsp;Mingwei Chen","doi":"10.1155/2022/7448481","DOIUrl":"https://doi.org/10.1155/2022/7448481","url":null,"abstract":"<p><p>Idiopathic pulmonary fibrosis (IPF) is a disease of progressive lung fibrosis with a high mortality rate. This study aimed to uncover the underlying molecular features for different types of IPF. IPF microarray datasets were retrieved from GEO databases. Weighted gene co-expression analysis (WGCNA) was used and identified subgroup-specific WGCNA modules. Infiltration-level immune cells in different subgroups of microenvironments were analyzed with CIBERSORT algorithms. The result is we classified 173 IPF cases into two subgroups based on gene expression profiles, which were retrieved from the GEO databases. The SGRQ score and age were significantly higher in C2 than in C1. Using WGCNA, five subgroup-specific modules were identified. M4 was mainly enriched by MAPK signaling, which was mainly expressed in C2; M1, M2, and M3 were mainly enriched by metabolic pathways and Chemokine signaling, and the pathway of M5 was phagosome inflammation; M1, M2, M3, and M5 were mainly expressed in C1. Utilizing the CIBERSORT, we showed that the number of M1 macrophage cells, CD8 T cells, regulatory T cells (Tregs), and Plasma cells was significantly different between C1 and C2. We found the molecular subgroups of IPF revealed that cases from different subgroups may have their unique patterns and provide novel information to understand the mechanisms of IPF itself.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":"7448481"},"PeriodicalIF":1.5,"publicationDate":"2022-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9308534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40595594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association of the <i>Interleukin-10-592C/A</i> Polymorphism and Cervical Cancer Risk: A Meta-Analysis.","authors":"Brehima Diakite, Yaya Kassogue, Mamoudou Maiga, Guimogo Dolo, Oumar Kassogue, Jonah Musa, Imran Morhason-Bello, Ban Traore, Cheick Bougadari Traore, Bakarou Kamate, Aissata Coulibaly, Sekou Bah, Sellama Nadifi, Robert Murphy, Jane L Holl, Lifang Hou","doi":"10.1155/2022/2319161","DOIUrl":"10.1155/2022/2319161","url":null,"abstract":"<p><p>A literature review showed some discrepancies regarding the association of <i>-592C/A</i> with the risk of cervical cancer. To allow more precise analysis of the data by increasing the number of cases studied and more acceptable generalization by considering results from different sources, the present meta-analysis was performed on available published studies that explored the relationship between SNP<i>-592C/A</i> of the <i>IL-10</i> gene and the risk of cervical cancer. Eleven available studies, including 4187 cases and 3311 controls, were included in this study investigating the relationship between the <i>-592C/A</i> polymorphism of <i>IL-10</i> and cervical cancer risk. Fixed-effects or random-effects models were performed with pooled odds ratios (ORs). Heterogeneity and bias tests were performed by the inconsistency test and funnel plot, respectively. The overall analysis showed an increased susceptibility to cervical cancer with the <i>-592C/A</i> polymorphism of the <i>IL-10</i> gene for the recessive model (OR = 1.30, 95% CI = 1.14-1.49), dominant model (OR = 1.36, 95% CI = 1.09-1.70), and additive model (OR = 1.25, 95% CI = 1.09-1.44). Regarding ethnicity, a significant association of the <i>-592C/A</i> polymorphism of the <i>IL-10</i> gene was linked to an elevated risk of cervical cancer for all genetic models (recessive, dominant, and additive) in the Asian populations and for the recessive and additive models in Caucasians with <i>P</i> < 0.05. The <i>-592C/A</i> polymorphism of the <i>IL-10</i> gene may be considered a risk factor for cervical cancer.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":"2022 ","pages":"2319161"},"PeriodicalIF":1.4,"publicationDate":"2022-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9296312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9277745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hsa-let-7c-5p, hsa-miR-130b-3p, and hsa-miR-142-3p as Novel miRNA Biomarkers for Melanoma Progression.","authors":"Xuerui Wu,&nbsp;Yu Wang,&nbsp;Chen Chen,&nbsp;Yadong Xue,&nbsp;Shuyun Zheng,&nbsp;Limin Cai","doi":"10.1155/2022/5671562","DOIUrl":"https://doi.org/10.1155/2022/5671562","url":null,"abstract":"<p><p>This study aimed to screen miRNA biomarkers for melanoma progression. Raw melanoma data were downloaded from the Gene Expression Omnibus (GSE34460, GSE35579, GSE18509, and GSE24996) and the Cancer Genome Atlas (TCGA). Then, all differentially expressed miRNAs (DEmiRNAs) between benign vs. primary, metastatic vs. benign, and metastatic vs. primary groups were obtained in the GSE34460 and GSE35579 datasets, and the miRNAs related to disease progression were further screened. Then, the miRNA-gene network was constructed, followed by enrichment, survival, and cluster analyses. Differentially expressed genes (DEGs), tumor-infiltrating immune cells, and tumor mutation burden (TMB) between subtypes were analyzed. miRNAs were verified in the GSE18509 and GSE24996 datasets. A total of 132 and 209 DEmiRNAs were obtained in the GSE34460 and GSE35579 datasets, respectively, and 27 DEmiRNAs related to disease progression were screened. hsa-miR-106b-5p, hsa-miR-27b-3p, and hsa-miR-141-3p had a higher degree and were regulated by numerous genes in the miRNA-gene network. Moreover, four miRNAs were associated with prognosis: hsa-let-7c-5p, hsa-miR-130b-3p, hsa-miR-142-3p, and hsa-miR-509-3p. Furthermore, the bidirectional hierarchical clustering of 27 miRNAs was classified into three subtypes, and TMB and four types of immune cells, including activated dendritic cells, naïve CD4 T cells, M1 macrophages, and plasma cells, showed significant differences among the three subtypes. The expression levels of most miRNAs in the GSE18509 and GSE24996 datasets were consistent with those in the training dataset. These miRNAs, including hsa-let-7c-5p, hsa-miR-130b-3p, and hsa-miR-142-3p, and activated dendritic cells, naïve CD4 T cells, M1 macrophages, and plasma cells may play vital roles in the pathogenesis of melanoma.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":"5671562"},"PeriodicalIF":1.5,"publicationDate":"2022-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40666568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics Analysis of Exercise-Related Biomarkers in Diabetes.","authors":"Xiaoju Bao,&nbsp;Jingyue Qiu,&nbsp;Qin Xuan,&nbsp;Xinming Ye","doi":"10.1155/2022/1273153","DOIUrl":"https://doi.org/10.1155/2022/1273153","url":null,"abstract":"<p><strong>Background: </strong>Exercise is a regular behavioral activity that not only helps to lose weight but also reduces the risk of cardiovascular and cerebrovascular diseases. Diabetes is a common disease that plagues human health. It is shown that regular exercise can improve the insulin sensitivity of diabetic patients and have an important function in adjuvant therapy.</p><p><strong>Methods: </strong>We downloaded the GSE101931 dataset from the Gene Expression Omnibus (GEO) database, 10 samples were obtained from the GSE101931 dataset, including 5 before exercise and 5 postexercise samples, and GEO2R was used to screen the differentially expressed genes (DEGs) exhibited by a heat map. Then, the enrichment analysis of DEGs in Gene Ontology (GO) function was analyzed by Metascape, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of DEGs was also analyzed by gene set enrichment analysis (GSEA). Next, the protein-protein interaction (PPI) network maps were drawn, and the hub genes were identified through Metascape. Finally, the expressions of the hub genes in the dataset were analyzed.</p><p><strong>Results: </strong>Totally, 116 upregulated DEGs and 1017 downregulated DEGs were identified from these data. These DEGs were mainly enriched in the platelet-derived growth factor receptor signaling pathway and mRNA processing. Then, the GSEA analysis showed that 6 KEGG pathways were associated with postexercise prediabetic samples, namely, ABC transporters, focal adhesion, MAPK signaling pathway, prion diseases, melanogenesis, and gap junction. Afterward, three hub genes (HSPA8, STIP1, and HSPH1) were highly expressed after exercise through the box plot analysis.</p><p><strong>Conclusion: </strong>A myriad of research results confirms that there is a certain connection between exercise and diabetes, which provides a favorable basis for emerging exercise into the treatment of diabetic patients.</p>","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":"1273153"},"PeriodicalIF":1.5,"publicationDate":"2022-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9259242/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40605955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Breast Cancer Prognosis Prediction and Immune Pathway Molecular Analysis Based on Mitochondria-Related Genes","authors":"Weixu Luo, Yuanshan Han, Xin Li, Zhuo Liu, P. Meng, Yuhong Wang","doi":"10.1155/2022/2249909","DOIUrl":"https://doi.org/10.1155/2022/2249909","url":null,"abstract":"Background Mitochondria play an important role in breast cancer (BRCA). We aimed to build a prognostic model based on mitochondria-related genes. Method Univariate Cox regression analysis, random forest, and the LASSO method were performed in sequence on pretreated TCGA BRCA datasets to screen out genes from a Gene Set Enrichment Analysis, Gene Ontology: biological process gene set to build a prognosis risk score model. Survival analyses and ROC curves were performed to verify the model by using the GSE103091 dataset. The BRCA datasets were equally divided into high- and low-risk score groups. Comparisons between clinical features and immune infiltration related to different risk scores and gene mutation analysis and drug sensitivity prediction were performed for different groups. Result Four genes, MRPL36, FEZ1, BMF, and AFG1L, were screened to construct our risk score model in which the higher the risk score, the poorer the prognosis. Univariate and multivariate analyses showed that the risk score was significantly associated with age, M stage, and N stage. The gene mutation probability in the high-risk score group was significantly higher than that in the low-risk score group. Patients with higher risk scores were more likely to die. Drug sensitivity prediction in different groups indicated that PF-562271 and AS601245 might be new inhibitors of BRCA. Conclusion We developed a new workable risk score model based on mitochondria-related genes for BRCA prognosis and identified new targets and drugs for BRCA research.","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47525843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association of Endothelin-Converting Enzyme and Endothelin-1 Gene Polymorphisms with Essential Hypertension in Malay Ethnics","authors":"Elnaz Salim, V. Ramachandran, Neda Ansari, P. Ismail, M. H. Mohamed, N. Mohamad, Liyana Najwa Inche Mat","doi":"10.1155/2022/9129960","DOIUrl":"https://doi.org/10.1155/2022/9129960","url":null,"abstract":"Objectives Endothelin-1 (ET-1), the most potent endogenous vasoconstrictor, generated by enzymatic cleavage catalyzed by an endothelin-converting enzyme (ECE), plays a significant role in the regulation of hypertension. Methods This study investigates the effect of endothelin-1 (Lys198Asn/rs5370) and ECE (rs212526 C/T) gene polymorphisms with essential hypertension (EH) among Malay ethnics. To determine the association of gene polymorphism, 177 hypertensives and controls (196) were genotyped using Taqman method. Results A significant difference was observed in ET-1 rs5370 and ECE rs212526 gene polymorphisms between EH and control subjects (P < 0.001). A significantly high body mass index (BMI), waist-to-hip ratio, fasting plasma glucose, hemoglobin A1c, systolic and diastolic blood pressure, and lipid profiles were observed among the EH patients when compared to controls (P < 0.05). Moreover, T allele (rs5370) carriers in males have a high risk for EH. There was no significant association between gender in ECE C/T polymorphisms (P > 0.05). Conclusion Based on our result, it is evident that the T allele of ET-1 rs5370 polymorphism and C allele of ECE rs212526 have a significant genetic risk factor in EH among Malay subjects, and BMI and age are associated with hypertension.","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45182150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Bioinformatical Identification of Potential Biomarkers in Heart Failure Diagnosis and Treatment","authors":"Xiaodong Sheng, Xiaoqi Jin, Yanqi Liu, Tao Fan, Zongcheng Zhu, Jing Jin, Guanqun Zheng, Zhixian Chen, Min Lu, Zhiqiang Wang","doi":"10.1155/2022/8727566","DOIUrl":"https://doi.org/10.1155/2022/8727566","url":null,"abstract":"Background Heart failure (HF) is defined as the inability of the heart's systolic and diastolic function to properly discharge blood flow from the veins to the heart. The goal of our research is to look into the possible mechanism that causes HF. Methods The GSE5406 database was used for screening the differentially expressed genes (DEGs). Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein-Protein Interaction (PPI) network were applied to analyze DEGs. Besides, cell counting Kit-8 (CCK-8) was conducted to observe the knockdown effect of hub genes on cell proliferation. Results Finally, 377 upregulated and 461 downregulated DEGs came out, enriched in the extracellular matrix organization and gap junction. According to GSEA results, Hoft cd4 positive alpha beta memory t cell bcg vaccine age 18–45 yo id 7 dy top 100 deg ex vivo up, Sobolev t cell pandemrix age 18–64 yo 7 dy dn, and so on were significantly related to gene set GSE5406. 7 hub genes, such as COL1A1, UBB, COL3A1, HSP90AA1, MYC, STAT3 and MAPK1, were selected from PPI networks. CCK-8 indicated silencing of STAT3 promoted the proliferation of H9C2 cells and silencing of UBB inhibited the proliferation of H9C2 cells. Conclusion Our analysis reveals that COL1A1, UBB, COL3A1, HSP90AA1, MYC, STAT3, and MAPK1 might promote the progression of HF and become the biomarkers for diagnosis and treatment of HF.","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45351459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy","authors":"Bing-Zhe Huang, Yang Jing-Jing, Xiao-Ming Dong, Zhuan Zhong, Xiao-Ning Liu","doi":"10.1155/2022/9792913","DOIUrl":"https://doi.org/10.1155/2022/9792913","url":null,"abstract":"Background We aimed to construct the lncRNA-associated competing endogenous RNA (ceRNA) network and distinguish feature lncRNAs associated with tendinopathy. Methods We downloaded the gene profile of GSE26051 from the Gene Expression Omnibus (GEO), including 23 normal samples and 23 diseased tendons. Differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) were identified, and functional and pathway enrichment analyses were performed. Protein-protein interaction (PPI) network was constructed and further analyzed by module mining. Moreover, a ceRNA regulatory network was constructed based on the identified lncRNA–mRNA coexpression relationship pairs and miRNA–mRNA regulation pairs. Results We identified 1117 DEmRNAs and 57 DElncRNAs from the GEO data. The downregulated DEmRNAs were particularly associated with muscle contraction and muscle filament, while the upregulated ones were linked to extracellular matrix organization and cell adhesion. From the PPI network, 11 modules were extracted. Genes in MCODE 2 (such as TPM4) were significantly involved in cardiomyopathy, and genes in MCODE 4 (such as COL4A3 and COL4A4) were involved in focal adhesion, ECM-receptor interaction, and PI3K-Akt signaling pathway. The ceRNA network contained 7 lncRNAs (MIR133A1HG, LINC01405, PRKCQ-AS1, C10orf71-AS1, MBNL1-AS1, HOTAIRM1, and DNM3OS), 63 mRNAs, and 41 miRNAs. Downregulated lncRNA MIR133A1HG could competitively bind with hsa-miR-659-3p and hsa-miR-218-1-3p to regulate the TPM3. Meanwhile, MIR133A1HG could competitively bind with hsa-miR-1179 to regulate the COL4A3. Downregulated C10orf71-AS1 could competitively bind with hsa-miR-130a-5p to regulate the COL4A4. Conclusions Seven important lncRNAs, particularly MIR133A1HG and C10orf71-AS1, were found associated with tendinopathy according to the lncRNA-associated ceRNA network.","PeriodicalId":12778,"journal":{"name":"Genetics research","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42529271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}