scholarly journals Bioinformatics Analysis Predicts ceRNA Regulatory Axes Related to Melanoma Pathogenesis

2021 ◽  
Author(s):  
Lina Liu ◽  
Feng Yang ◽  
Saiyun Lei
Keyword(s):  
Cutaneous Melanoma ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cerna Network ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Incidence And Mortality ◽  
Malignant Skin ◽  
Clinical Verification ◽  
Geo Database

Abstract Background Melanoma is a highly malignant skin tumour, with an incidence and mortality rates accounting for approximately 5% and >75% of all tumours, respectively. In the present study, we aimed to screen mRNAs, microRNAs, and circRNAs related to the pathogenesis of melanoma via bioinformatics methods. Materials and methods The microarray data correlating with melanoma were obtained from the GEO database, and the differentially expressed genes between melanomatissues and non-melanoma tissues were screened using GEO2R. Moreover, the Hub genes were screened using the STRING database, Cytoscape software, and GEPIA database. The DAVID database was used for gene enrichment analysis. Thereafter, the ceRNA network diagram was constructed using the starBase database and was analysed for survival in order to predict the molecular markers for diagnosis and treatment of skin cutaneous melanoma; the most probable ceRNA mechanism was screened via pan-cancer analysis. Furthermore, the ceRNA network was verified using the GEPIA and UALCAN databases. Results In total, 266, 20, and 10 differentially expressed mRNAs, microRNAs, and circRNA10 were screened. Using Cytoscape software, 59 Hub and 31 key genes were screened, followed by construction of the ceRNA and ceRNA-gene enrichment analysis networks. Conclusion Clinical verification revealed that SIPA1L1 could regulate the expression of DSC3 by sponge adsorption of has-miR-106b and has-miR-20b, and thereby affect the pathogenesis and progression of skin cutaneous melanoma.

scholarly journals Joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in gastric cancer

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhi Lv ◽  
Liping Sun ◽  
Qian Xu ◽  
Chengzhong Xing ◽  
Yuan Yuan
Keyword(s):  
Gastric Cancer ◽  
Mrna Expression ◽  
Expression Analysis ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Joint Analysis ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

Abstract Background N6-methyladenosine (m6A) modification might be closely associated with the genesis and development of gastric cancer (GC). Currently, the evidence established by high-throughput assay for GC-related m6A patterns based on long non-coding RNAs (lncRNAs) remains limited. Here, a joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in GC was performed to explore the regulatory roles of m6A modification in lncRNAs. Methods Three subjects with primary GC were enrolled in our study and paired sample was randomly selected from GC tissue and adjacent normal tissue for each case. Methylated RNA Immunoprecipitation NextGeneration Sequencing (MeRIP-Seq) and Microarray Gene Expression Profiling was subsequently performed. Then co-expression analysis and gene enrichment analysis were successively conducted. Results After data analysis, we identified 191 differentially m6A-methylated lncRNAs, 240 differentially expressed lncRNAs and 229 differentially expressed mRNAs in GC. Furthermore, four differentially m6A-methylated and expressed lncRNAs (dme-lncRNAs) were discovered including RASAL2-AS1, LINC00910, SNHG7 and LINC01105. Their potential target genes were explored by co-expression analysis. And gene enrichment analysis suggested that they might influence the cellular processes and biological behaviors involved in mitosis and cell cycle. The potential impacts of these targets on GC cells were further validated by CCLE database and literature review. Conclusions Four novel dme-lncRNAs were identified in GC, which might exert regulatory roles on GC cell proliferation. The present study would provide clues for the lncRNA m6A methylation-based research on GC epigenetic etiology and pathogenesis.

scholarly journals Differentially Expressed Circular Non-coding RNAs in Atherosclerotic Aortic Vessels and Their Potential Functions in Endothelial Injury

2021 ◽  
Vol 8 ◽  
Author(s):  
Houwei Li ◽  
Xue Liu ◽  
Na Sun ◽  
Tianshuo Wang ◽  
Jia Zhu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Enrichment Analysis ◽  
Potential Functions ◽  
Endothelial Injury ◽  
Differentially Expressed ◽  
Vascular Endothelial ◽  
Rt Pcr ◽  
Potential Target ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

Background: Circular non-coding RNA (circRNA) has a variety of biological functions. However, the expression profile and potential effects of circRNA on atherosclerosis (AS) and vascular endothelial injury have not been fully elucidated. This study aims to identify the differentially expressed circRNAs in atherosclerotic aortic vessels and predict their potential functions in endothelial injury.Method: ApoE-/- mice were fed with high-fat diet for 12 weeks to induce AS. Atherosclerotic plaques were evaluated by H&E and Masson staining and immunohistochemistry; differentially expressed circRNAs were detected by Arraystar Circular RNA Microarray and verified by RT-PCR; the potential target mircoRNAs of circRNAs were predicted by miRanda, Tarbase, Targetscan and their expression changes were verified by RT-PCR; the potential target genes of mircoRNAs were predicted by Targetscan and verified by Western blot; the signaling pathways that they might annotate or regulate and their potential functions in vascular endothelial injury were predicted by gene enrichment analysis.Results: Fifty two circRNAs were up-regulated more than twice and 47 circRNAs were down-regulated more than 1.5 times in AS aortic vessels. Mmmu_circRNA_36781 and 37699 were up-regulated both in AS aortic vessels and H2O2-treated mouse aortic endothelial cells (MAECs). The expression of miR-30d-3p and miR-140-3p, the target microRNA of circRNA_37699 and circRNA_36781, were downregulated both in AS vessels and H2O2-treated MAECs. On the contrary, MKK6 and TP53RK, the potential target gene of miR-140-3p and miR-30d-3p, were upregulated both in AS aortic roots and H2O2-treated MAECs. Besides, gene enrichment analysis showed that MAPK and PI3K-AKT signaling pathway were the most potential signaling pathways regulated by the differentially expressed circRNAs in atherosclerosis.Conclusions: Mmu_circRNA_36781 (circRNA ABCA1) and 37699 (circRNA KHDRBS1) were significantly up-regulated in AS aortic vessels and H2O2-treated MAECs. They have potential regulatory effects on atherosclerosis and vascular endothelial injury by targeting miR-30d-3p-TP53RK and miR-140-3p-MKK6 axis and their downstream signaling pathways.

scholarly journals Effect of flapless osteoperforation-assisted tooth movement on atrophic alveolar ridge: Histomorphometric and gene-enrichment analysis

2017 ◽  
Vol 88 (1) ◽  
pp. 82-90 ◽  
Author(s):  
Ji-Won Lee ◽  
Jung-Yul Cha ◽  
Ki-Ho Park ◽  
Yoon-Goo Kang ◽  
Su-Jung Kim
Keyword(s):  
Signaling Pathway ◽  
Tooth Movement ◽  
Osteoclast Differentiation ◽  
Wnt Signaling Pathway ◽  
Enrichment Analysis ◽  
Tissue Response ◽  
Alveolar Ridge ◽  
Mineral Density ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

ABSTRACT Objective: To investigate the effect of flapless osteoperforation on the tissue response of the atrophic alveolar ridge affected by orthodontic tooth movement (OTM). Materials and Methods: An atrophic alveolar ridge model was established in the mandibular quadrants of eight beagle dogs. As a split-mouth design, the quadrants were randomly divided into group C (OTM only) and group OP (OTM with flapless osteoperforation). The rate of OTM for 10 weeks was compared between groups, and micro-CT-based histomorphometric analysis and RNA-sequencing-based gene-enrichment analysis were performed targeting the atrophic ridge. Results: Group OP displayed more rapid tooth movement with lower bone mineral density and higher trabecular fraction in the atrophic ridge than did group C, showing no intergroup difference of total ridge volume. As contributing biological functional pathways in group OP, the genes related to osteoclast differentiation and TNF signaling pathway were up-regulated and those associated with Wnt signaling pathway and AMPK signaling pathway were down-regulated. Conclusions: Flapless osteoperforation facilitated the rate of OTM toward the atrophic ridge, maintaining low bone density, whereas it did not increase the volume of the atrophic ridge.

scholarly journals LINC01018 and SMIM25 sponged miR-182-5p in endometriosis revealed by the ceRNA network construction

2020 ◽  
Vol 34 ◽  
pp. 205873842097630
Author(s):  
Li Jiang ◽  
Mengmeng Zhang ◽  
Sixue Wang ◽  
Yuzhen Xiao ◽  
Jingni Wu ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Protein Protein Interaction ◽  
Cerna Network ◽  
Non Coding Rna ◽  
Differentially Expressed Mirnas ◽  
Long Non Coding Rna

The current study intended to explore the interaction of the long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) under the background of competitive endogenous RNA (ceRNA) network in endometriosis (EMs). The differentially expressed miRNAs (DEmiRs), differentially expressed lncRNA (DELs), and differentially expressed genes (DEGs) between EMs ectopic (EC) and eutopic (EU) endometrium based on three RNA-sequencing datasets (GSE105765, GSE121406, and GSE105764) were identified, which were used for the construction of ceRNA network. Then, DEGs in the ceRNA network were performed with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) analysis. Besides, the DEmiRs in the ceRNA network were validated in GSE124010. And the target DELs and DEGs of verified DEmiRs were validated in GSE86534. The correlation of verified DEmiRs, DEGs, and DELs was explored. Moreover, gene set enrichment analysis (GSEA) was applied to investigate the function of verified DEmiRs, DEGs, and DELs. Overall, 1352 DEGs and 595 DELs from GSE105764, along with 27 overlapped DEmiRs between GSE105765 and GSE121406, were obtained. Subsequently, a ceRNA network, including 11 upregulated and 16 downregulated DEmiRs, 7 upregulated and 13 downregulated DELs, 48 upregulated and 46 downregulated DEGs, was constructed. The GO and KEGG pathway analysis showed that this ceRNA network probably was associated with inflammation-related pathways. Furthermore, hsa-miR-182-5p and its target DELs (LINC01018 and SMIM25) and DEGs (BNC2, CHL1, HMCN1, PRDM16) were successfully verified in the validation analysis. Besides, hsa-miR-182-5p was significantly negatively correlated with these target DELs and DEGs. The GSEA analysis implied that high expression of LINC01018, SMIM25, and CHL1, and low expression of hsa-miR-182-5p would activate inflammation-related pathways in endometriosis EU samples. LINC01018 and SMIM25 might sponge hsa-miR-182-5p to upregulate downstream genes such as CHL1 to promote the development of endometriosis.

scholarly journals Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions

2008 ◽  
Vol 36 (7) ◽  
pp. e43-e43 ◽  
Author(s):  
K. De Preter ◽  
R. Barriot ◽  
F. Speleman ◽  
J. Vandesompele ◽  
Y. Moreau
Keyword(s):  
High Resolution ◽  
Enrichment Analysis ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Gene Sets

scholarly journals A Network Pharmacology Approach to Uncover the Multiple Mechanisms of Hedyotis diffusa Willd. on Colorectal Cancer

2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Xinkui Liu ◽  
Jiarui Wu ◽  
Dan Zhang ◽  
Kaihuan Wang ◽  
Xiaojiao Duan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Network Analysis ◽  
Chinese Herb ◽  
Endocrine System ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Hedyotis Diffusa

Background. As one of the most frequently diagnosed cancer diseases globally, colorectal cancer (CRC) remains an important cause of cancer-related death. Although the traditional Chinese herb Hedyotis diffusa Willd. (HDW) has been proven to be effective for treating CRC in clinical practice, its definite mechanisms have not been completely deciphered. Objective. The aim of our research is to systematically explore the multiple mechanisms of HDW on CRC. Methods. This study adopted the network pharmacology approach, which was mainly composed of active component gathering, target prediction, CRC gene collection, network analysis, and gene enrichment analysis. Results. The network analysis showed that 10 targets might be the therapeutic targets of HDW on CRC, namely, HRAS, PIK3CA, KRAS, TP53, APC, BRAF, GSK3B, CDK2, AKT1, and RAF1. The gene enrichment analysis implied that HDW probably benefits patients with CRC by modulating pathways related to cancers, infectious diseases, endocrine system, immune system, nervous system, signal transduction, cellular community, and cell motility. Conclusions. This study partially verified and predicted the pharmacological and molecular mechanism of HDW against CRC from a holistic perspective, which will also lay a foundation for the further experimental research and clinical rational application of HDW.

scholarly journals Network pharmacology-based elucidation of the molecular mechanism underlying the anti-migraine effect of Asari Radix et Rhizoma

2021 ◽  
Vol 18 (10) ◽  
pp. 2067-2074
Author(s):  
Yun-Bin Jiang ◽  
Mei Zhong ◽  
Ting Huang ◽  
Zhong-Hua Dai ◽  
Xing-Bao Tao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Scientific Basis ◽  
Network Pharmacology ◽  
Overlapping Genes ◽  
Hub Genes ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Tnf Gene

Purpose: To determine the molecular mechanism involved in the anti-migraine effect of Asari Radix et Rhizoma (ARR) using network pharmacology. Methods: The compounds present in ARR were identified through information retrieval from literature and public databases, and were screened based on absorption, distribution, metabolism, excretion and toxicity. Target genes related to the selected compounds and migraine were identified or predicted from public databases. Hub genes in ARR against migraine were identified through analysis of interactions in overlapping genes between compounds and migraine target genes, based on STRING database. Gene enrichment analysis of overlapping genes was performed using Database for Annotation, Visualization and Integrated Discovery. Results: A total of 138 compounds were selected as potential bioactive compounds in ARR. Target genes related to the selected compounds (611 genes) and migraine (278 genes) were obtained, including 71 overlapping genes. The hub genes in the anti-migraine effect of ARR were BDNF, IL6, COMT, APP and TNF. Gene enrichment analysis showed the top 10 biological processes or pathways involved in the mechanism of anti-migraine action of ARR. The tissue source of the overlapping genes was not limited to the brain. The results from gene enrichment analysis revealed that the effect of ARR on migraine was holistic, which is characteristic of traditional Chinese medicines. Conclusion: Network pharmacology has been used to decipher the molecular mechanism involved in the action of ARR against migraine. The results provide a scientific basis for the clinical effect of ARR on migraine.

scholarly journals A Potential ceRNA Network for Neurological Damage in Preterm Infants

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Jin Huang ◽  
Xuejing Liang ◽  
Zhenyu Cai
Keyword(s):  
Brain Injury ◽  
Preterm Infants ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Neurological Injury ◽  
Ppi Network ◽  
Neurological Damage ◽  
Injury Group ◽  
Differentially Expressed Mirnas ◽  
Geo Database

Objective. This study is aimed at identifying key genes involved in neurological damage in preterm infants and at determining their potential circRNA-miRNA-mRNA regulatory mechanisms. Methods. Differentially expressed miRNAs, mRNAs, and circRNAs were downloaded from the GEO database. GO and KEGG enrichment analyses were used to determine possible relevant functions of differentially expressed mRNAs. The TTRUST database was used to predict differential TF-mRNA regulatory relationships. Then, CircMIR, miRDB, TargetScan and miRTarBase were then used to map circRNA/miRNA-TF/mRNA interaction networks. Finally, GSEA enrichment analysis was performed on the core transcription factors. Results. A total of 640 mRNAs, 139 circRNAs, and 206 differentially expressed miRNAs associated with neurological injury in preterm infants were obtained. Based on the findings of Cytoscape and PPI network analysis, the hsa_circ_0008439-hsa-mir-3665-STAT3-MMP3 regulatory axis was established. GSEA analysis revealed that suppressed expression levels of STAT3 were associated with upregulated oxidative phosphorylation pathways in the neurological injury group of preterm infants. Conclusions. The circRNA-miRNA-TF-mRNA regulatory network of neurological injury in preterm infants can be used to elucidate on the pathogenesis of brain injury and help us with the early detection of brain injury in preterm infants.

scholarly journals Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10529
Author(s):  
Yueqi Li ◽  
Wudi Wei ◽  
Sanqi An ◽  
Junjun Jiang ◽  
Jinhao He ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
R Package ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Next Generation Sequencing Technology ◽  
Talaromyces Marneffei ◽  
Kegg Analysis ◽  
Cerna Network

Background Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs, which have been considered to play a significant role in pathogen-host innate immune response. However, knowledge of ceRNA regulatory networks in Talaromyces marneffei (TM)-macrophages is still limited. Methods Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages. The R package DESeq2 was used to identify differentially expressed lncRNA, miRNA and mRNA. The R package GOseq was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and the ceRNA network of lncRNA–miRNA–mRNA interaction was constructed in Cytoscape. Similarly, functional enrichment analysis on mRNA in the ceRNA network. Finally, two mRNAs and four lncRNAs in the ceRNA network were randomly selected to verify the expression using qRT-PCR. Results In total, 119 lncRNAs, 28 miRNAs and 208 mRNAs were identified as differentially expressed RNAs in TM-infected macrophages. The constructed ceRNA network contains 38 lncRNAs, 10 miRNAs and 45 mRNAs. GO and KEGG analysis of mRNA in the ceRNA network indicated that activated pathways in TM-infected macrophages were related to immunity, inflammation and metabolism. The quantitative validation of the expression of four randomly selected differentially expressed lncRNAs, AC006252.1, AC090197.1, IL6R-AS1, LINC02009 and two mRNAs, CSF1, NR4A3 showed that the expression levels were consistent with those in the RNA-sequencing. Conclusions The ceRNA network related to immunity, inflammation and metabolism plays an important role in TM-macrophage interaction. This study may provide effective and novel insights for further understanding the underlying mechanism of TM infection.

Sign in / Sign up

Export Citation Format

Share Document