scholarly journals BioinformaticsAnalysis of the Muscle-invasive Bladder Cancer Subtypes

1970 ◽  
Vol 2 (2) ◽  
Author(s):  
Wenbin Xu ◽  
Weiying Zheng ◽  
Hong Xia ◽  
Lin Hua
Keyword(s):  
Extracellular Matrix ◽  
Bladder Cancer ◽  
Inflammatory Response ◽  
Differentially Expressed Genes ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Cancer Subtypes ◽  
Pathway Enrichment

Objective In order to improve the accuracy in distinguishing subtypes of bladder cancer and to explore its potential therapeutic targets, we identify differences between two kinds of bladder cancer subtypes (basal-like and luminal) in molecular mechanism and molecular characteristics based on the bioinformatics analysis. Methods In this study, the RMA (robust multichip averaging) was applied to normalize the mRNA profile which included 22 samples from basal-like subtype and 132 from luminal subtype, and the differential expression analysis of genes with top 1000 highest standard deviation was performed. Then, the Gene Ontology and KEGG pathway enrichment analysis of differentially expressed genes was performed. In addition, the protein-protein interactions networks analysis for the top 100 most significant differentially expressed genes was performed. Results A total of 742 differentially expressed genes distinguishing basal-like and luminal subtypes were found, of which 405 were up-regulated and 337 genes were down-regulated in basal-like subtype. GO enrichment analysis showed that differentially expressed genes were significantly enriched in the extracellular matrix, chemotaxis and inflammatory response. KEGG pathway enrichment analysis showed that the differentially expressed genes were significantly enriched in the pathway of extracellular matrix receptor interaction. The hub proteins we founded in protein-protein interaction networks were LNX1, MSN and PPARG. Conclusion In this study, the mainly difference of molecular mechanism between basal-like and luminal subtypes are alteration in extracellular matrix region, cell chemotaxis and inflammatory response. Genes such as LNX1, MSN and PPARG were forecast to play important roles in the classification of bladder carcinoma subtypes.

Identification of Differentially Expressed Genes and Signaling Pathways Related to Ovarian Endometriosis by Integrated Bioinformatics Analysis

2020 ◽  
Author(s):  
Kainan Lin ◽  
Zhenyan Pan ◽  
Renke He ◽  
Hanchu Wang ◽  
Kai Zhou ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Go Analysis ◽  
Pathway Enrichment

Abstract Purpose: Endometriosis was a common gynecological disease, however, the specific mechanism and the key molecules of endometriosis remained uncertain. This study aimed to single out key genes associated with poor prognosis, and further uncover underlying mechanisms.Methods: Data regarding mRNA expression profiles used in this study were retrieved from the Gene Expression Omnibus (GEO) database, a total of three mRNA expression profiles were included for subsequent analysis (GSE31515, GSE58178 and GSE120103). Then, we conducted Gene Ontology analysis (GO analysis), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and protein-protein interaction (PPI) analysis by the software R.Results: A total of 304 differentially expressed genes (DEGs) between endometriosis tissues and normal endometrium tissues were identified in integrated analysis, including 185 up-regulated genes and 119 down-regulated genes. GO analysis reveals that the DEGs of endometriosis were closely associated with molecular origin of bacteria. KEGG pathway enrichment analysis indicates that the DEGs were mainly involved in AGE-RAGE signaling pathway in diabetic complications. In addition, PPI of these DEGs was visualized by Cytoscape platform with utilization of Search Tool for the Retrieval of Interacting Genes (STRING). PPI analysis identifies 10 potential DEGs-related protein targets, including CCND1, IL6, CCL2, COL1A2, PTGS2, VCAM1, COL3A1, ELN, SERPINE1, HSP90B1. Conclusion: In conclusion, the present study reveals that bacterial contamination, defect of female reproductive system development, retrograde menstruation and the AGE-RAGE signaling pathway may be involved in the development of endometriosis In addition, these identified DEGs may be of clinical significance for the diagnosis and treatment of the endometriosis.

scholarly journals Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae) with comparative transcriptomics

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4448 ◽  
Author(s):  
Dingxuan He ◽  
Pin Guo ◽  
Paul F. Gugger ◽  
Youhao Guo ◽  
Xing Liu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Floating Leaves

Many plant species exhibit different leaf morphologies within a single plant, or heterophylly. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, at different stages of development, were sequenced using high-throughput sequencing (RNA-Seq), in order to aid gene discovery and functional studies of genes involved in heterophylly. A total of 81,103 unigenes were identified in submerged and floating leaves and 6,822 differentially expressed genes (DEGs) were identified by comparing samples at differing time points of development. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways. A total of 24,025 differentially expressed genes were involved in carbon metabolic pathways, biosynthesis of amino acids, ribosomal processes, and plant-pathogen interactions. In particular, KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. The high-throughput transcriptomic results presented here highlight the potential for understanding the molecular mechanisms underlying heterophylly, which is still poorly understood. Further, these data provide a framework to better understand heterophyllous leaf development in P. octandrus via targeted studies utilizing gene cloning and functional analyses.

scholarly journals Transcriptomic analysis of Procambarus clarkii affected by “Black May” disease

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guoqing Shen ◽  
Xiao Zhang ◽  
Jie Gong ◽  
Yang Wang ◽  
Pengdan Huang ◽  
...  
Keyword(s):  
Procambarus Clarkii ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Apoptosis Pathway ◽  
Pathway Enrichment ◽  
Cellular Processes ◽  
Expression Of Genes ◽  
Muscle Tissues

AbstractEach year from April to May, high mortality rates are reported in red swamp crayfish (Procambarus clarkii) cultured in Jiangsu and other regions, in China, and this phenomenon has come to be known as “Black May” disease (BMD). Therefore, in order to investigate the possible causes of this disease, this study gathered BMD-affected P. clarkii samples and performed transcriptome analysis on hepatopancreas, gill, and muscle tissues. A total of 19,995,164, 149,212,804, and 222,053,848 clean reads were respectively obtained from the gills, muscle, and hepatopancreas of BMD-affected P. clarkii, and 114,024 unigenes were identified. The number of differentially expressed genes (DEGs) in gill, muscle, and hepatopancreas was 1703, 964, and 476, respectively. GO and KEGG enrichment analyses of the DEGs were then conducted. Based on KEGG pathway enrichment analysis, the most significantly differentially expressed pathways were mainly those involved with metabolism, human disease, and cellular processes. Further analysis of the significantly DEGs revealed that they were mainly related to the mitochondrial-mediated apoptosis pathway and that the expression of these DEGs was mostly down-regulated. Moreover, the expression of genes related to immune and metabolism-related pathways was also significantly down-regulated, and these significantly-inhibited pathways were the likely causes of P. clarkii death. Therefore, our results provide a basis for the identification of BMD causes.

scholarly journals Comparative transcriptomic analysis of heterophylly of the aquatic plant Potamogeton octandrus (Potamogetonaceae)

2017 ◽  
Author(s):  
Dingxuan He ◽  
Pin Guo ◽  
Paul F Gugger ◽  
Youhao Guo ◽  
Xing Liu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
High Throughput ◽  
Leaf Development ◽  
Aquatic Plant ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Functional Studies ◽  
Floating Leaves

Many plant species exhibit heterophylly, displaying different leaves upon a single plant. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, were sequenced using a high-throughput sequencing technique (RNA-Seq), which aims to assist with the gene discovery and functional studies of genes involved in heterophyllous leaf development. A total of 81,103 unigenes were identified from the submerged and floating leaves, and a total of 6,822 differentially expressed genes (DEGs) were identified by comparing the samples from each developmental stage. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways (p-value < 10-5). A total of 24,025 differentially expressed genes were involved in the carbon metabolic pathway, biosynthesis of amino acids, ribosomes, and plant-pathogen interaction. KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. This study describes the initial results of the high-throughput transcriptome sequencing of heterophylly. Understanding the transcriptomes of floating and submerged leaves of the aquatic plant P. octandrus will assist with gene cloning and functional studies of genes involved in leaf development. This is especially the case with those involved in heterophyllous leaf development.

scholarly journals Identification of Potential Autophagy-Related Genes in Steroid-Induced Osteonecrosis of the Femoral Head

2021 ◽  
Author(s):  
XueZhen LIANG ◽  
Di LUO ◽  
Yan-Rong CHEN ◽  
Jia-Cheng LI ◽  
Bo-Zhao YAN ◽  
...  
Keyword(s):  
Femoral Head ◽  
Correlation Analysis ◽  
Bioinformatics Analysis ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Hub Genes ◽  
R Software ◽  
Pathway Enrichment

Abstract Purpose: Steroid-induced osteonecrosis of the femoral head (SONFH) was a refractory orthopedic hip joint disease in the young and middle-aged people. Previous experimental studies had shown that autophagy might be involved in the pathological process of SONFH, but the pathogenesis of autophagy in SONFH remained unclear. We aim to identify and validate the key potential autophagy-related genes of SONFH to further illustrate the mechanism of autophagy in SONFH through bioinformatics analysis. Methods: The mRNA expression profile dataset GSE123568 was download from Gene Expression Omnibus (GEO) database, including 10 non-SONFH (following steroid administration) samples and 30 SONFH samples. The autophagy-related genes were obtained from the Human Autophagy Database (HADb). The autophagy-related genes of SONFH were screened by intersecting GSE123568 dataset with autophagy genes. The differentially expressed autophagy-related genes of SONFH were identified by R software. Besides, the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted for the differentially expressed autophagy-related genes of SONFH by R software. Then, the correlation analysis between the expression levels of differentially expressed autophagy-related genes of SONFH was confirmed by R software. Moreover, the protein–protein interaction (PPI) network were analyzed by the Search Tool for the Retrieval of Interacting Genes (STRING), and the significant gene cluster modules were identified by the MCODE Cytoscape plugin, and hub genes of differentially expressed autophagy-related genes of SONFH were screened by the CytoHubba Cytoscape plugin. Finally, the expression levels of hub genes of differentially expressed autophagy-related genes of SONFH was validated in hip articular cartilage specimens from necrosis femur head (NFH) by GSE74089 dataset. Results: A total of 34 differentially expressed autophagy-related genes were identified between the peripheral blood of SONFH samples and non-SONFH Samples based on the defined criteria, including 25 up-regulated genes and 9 down-regulated genes. The GO and KEGG pathway enrichment analysis revealed that these 34 differentially expressed autophagy-related genes of SONFH were concentrated in death domain receptors, FOXO signaling pathway and apoptosis. The correlation analysis revealed a significant correlation among the 34 differentially expressed autophagy-related genes of SONFH. The PPI results demonstrated that the 34 differentially expressed autophagy-related genes interacted with each other. There were 10 hub genes identified by the MCC algorithms of Cytohubba. The results of GSE74089 dataset showed TNFSF10, PTEN and CFLAR were significantly upregulated while BCL2L1 were significantly downregulated in the hip cartilage specimens, which were consistent with the GSE123568 dataset. Conclusions: There were 34 potential autophagy-related genes of SONFH identified using bioinformatics analysis. TNFSF10, PTEN, CFLAR and BCL2L1 might serve as potential drug targets and biomarkers by regulating autophagy. These results would expand new insights into the autophagy-related understanding of SONFH and might be useful in the diagnosis and prognosis of SONFH.

scholarly journals Construction of a circRNA-miRNA-mRNA network based on competitive endogenous RNA reveals the key pathways and central genes of osteosarcoma in vivo

2021 ◽  
Author(s):  
Zhihao Chen ◽  
Xi Wang ◽  
Liubing Li ◽  
Mingxiao Han ◽  
Min Wang ◽  
...  
Keyword(s):  
Protein Modification ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Micro Rna ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Go Annotation ◽  
Pathway Enrichment ◽  
Ppi Networks

Abstract Circular RNAs (circRNAs) play important roles in a variety of pathological functions. However, the potential functions and detailed mechanisms of circRNAs in osteosarcoma (OS) have not been fully elucidated. In this study, the circRNA, micro RNA (miRNA), and messenger RNA (mRNA) expression profile of human OS was investigated based on the raw microarray data GSE140256, GSE65071 and GSE16088 in Gene Expression Omnibus (GEO) datasets, and seven differentially-expressed circRNAs (DEcircRNAs), 166 differentially-expressed miRNAs (DEmiRNAs), and 175 differentially-expressed mRNAs (DEmRNAs) were identified in total. FunRich was employed to analyze the differentially-expressed transcription factors on the basis of identified DEmiRNAs. In addition, the Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to further study biological functions of the DEmRNAs. Interestingly, post-translational protein modification, collagen-containing extracellular matrix, and single-stranded DNA binding were the most significant pathways enriched for DEmRNAs in GO annotation analysis. Meanwhile, in KEGG pathway enrichment analysis, complement and coagulation cascades, RNA transport and drug metabolism − other enzymes were the most significantly enriched pathways of DEmRNAs in OS. We constructed circRNA-miRNA-mRNA and protein–protein interaction (PPI) networks that may be associated with pathological processes of OS. Finally, we also revealed the pattern of tumor-infiltrating immune cells in OS and further explored the ceRNA networks we constructed in which we found that COL1A1 and RAN were significantly correlated with overall survival in patients with osteosarcoma (p < 0.05). To our knowledge, this study provides the first profile analysis of DEcircRNAs, DEmiRNAs, and DEmRNAs with OS in vivo and reveals a novel idea for understanding the pathogenesis of OS.

scholarly journals Comparative transcriptomic analysis of heterophylly of the aquatic plant Potamogeton octandrus (Potamogetonaceae)

2017 ◽  
Author(s):  
Dingxuan He ◽  
Pin Guo ◽  
Paul F Gugger ◽  
Youhao Guo ◽  
Xing Liu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
High Throughput ◽  
Leaf Development ◽  
Aquatic Plant ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Pathway Enrichment ◽  
Functional Studies ◽  
Floating Leaves

Many plant species exhibit heterophylly, displaying different leaves upon a single plant. The molecular mechanisms regulating this phenomenon, however, have remained elusive. In this study, the transcriptomes of submerged and floating leaves of an aquatic heterophyllous plant, Potamogeton octandrus Poir, were sequenced using a high-throughput sequencing technique (RNA-Seq), which aims to assist with the gene discovery and functional studies of genes involved in heterophyllous leaf development. A total of 81,103 unigenes were identified from the submerged and floating leaves, and a total of 6,822 differentially expressed genes (DEGs) were identified by comparing the samples from each developmental stage. KEGG pathway enrichment analysis categorized these unigenes into 128 pathways (p-value < 10-5). A total of 24,025 differentially expressed genes were involved in the carbon metabolic pathway, biosynthesis of amino acids, ribosomes, and plant-pathogen interaction. KEGG pathway enrichment analysis categorized a total of 70 DEGs into plant hormone signal transduction pathways. This study describes the initial results of the high-throughput transcriptome sequencing of heterophylly. Understanding the transcriptomes of floating and submerged leaves of the aquatic plant P. octandrus will assist with gene cloning and functional studies of genes involved in leaf development. This is especially the case with those involved in heterophyllous leaf development.

Systematic Investigation of Quercetin for Treating Cardiovascular Disease Based on Network Pharmacology

2019 ◽  
Vol 22 (6) ◽  
pp. 411-420 ◽  
Author(s):  
Xian-Jun Wu ◽  
Xin-Bin Zhou ◽  
Chen Chen ◽  
Wei Mao
Keyword(s):  
Cardiovascular Disease ◽  
Cardiovascular Diseases ◽  
Signaling Pathway ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Therapeutic Effects ◽  
Pathway Enrichment ◽  
Compound Target

Aim and Objective: Cardiovascular disease is a serious threat to human health because of its high mortality and morbidity rates. At present, there is no effective treatment. In Southeast Asia, traditional Chinese medicine is widely used in the treatment of cardiovascular diseases. Quercetin is a flavonoid extract of Ginkgo biloba leaves. Basic experiments and clinical studies have shown that quercetin has a significant effect on the treatment of cardiovascular diseases. However, its precise mechanism is still unclear. Therefore, it is necessary to exploit the network pharmacological potential effects of quercetin on cardiovascular disease. Materials and Methods: In the present study, a novel network pharmacology strategy based on pharmacokinetic filtering, target fishing, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, compound-target-pathway network structured was performed to explore the anti- cardiovascular disease mechanism of quercetin. Results:: The outcomes showed that quercetin possesses favorable pharmacokinetic profiles, which have interactions with 47 cardiovascular disease-related targets and 12 KEGG signaling pathways to provide potential synergistic therapeutic effects. Following the construction of Compound-Target-Pathway (C-T-P) network, and the network topological feature calculation, we obtained top 10 core genes in this network which were AKT1, IL1B, TNF, IL6, JUN, CCL2, FOS, VEGFA, CXCL8, and ICAM1. KEGG pathway enrichment analysis. These indicated that quercetin produced the therapeutic effects against cardiovascular disease by systemically and holistically regulating many signaling pathways, including Fluid shear stress and atherosclerosis, AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, MAPK signaling pathway, IL-17 signaling pathway and PI3K-Akt signaling pathway.

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

scholarly journals Lipidomics profiling of goose granulosa cell model of stearoyl-CoA desaturase function identifies a pattern of lipid droplets associated with follicle development

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xin Yuan ◽  
Shenqiang Hu ◽  
Liang Li ◽  
Chunchun Han ◽  
Hehe Liu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Lipid Droplets ◽  
Cell Model ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Follicle Development ◽  
Microscopy Analysis ◽  
Stearoyl Coa Desaturase ◽  
Underlying Mechanisms

Abstract Background Despite their important functions and nearly ubiquitous presence in cells, an understanding of the biology of intracellular lipid droplets (LDs) in goose follicle development remains limited. An integrated study of lipidomic and transcriptomic analyses was performed in a cellular model of stearoyl-CoA desaturase (SCD) function, to determine the effects of intracellular LDs on follicle development in geese. Results Numerous internalized LDs, which were generally spherical in shape, were dispersed throughout the cytoplasm of granulosa cells (GCs), as determined using confocal microscopy analysis, with altered SCD expression affecting LD content. GC lipidomic profiling showed that the majority of the differentially abundant lipid classes were glycerophospholipids, including PA, PC, PE, PG, PI, and PS, and glycerolipids, including DG and TG, which enriched glycerophospholipid, sphingolipid, and glycerolipid metabolisms. Furthermore, transcriptomics identified differentially expressed genes (DEGs), some of which were assigned to lipid-related Gene Ontology slim terms. More DEGs were assigned in the SCD-knockdown group than in the SCD-overexpression group. Integration of the significant differentially expressed genes and lipids based on pathway enrichment analysis identified potentially targetable pathways related to glycerolipid/glycerophospholipid metabolism. Conclusions This study demonstrated the importance of lipids in understanding follicle development, thus providing a potential foundation to decipher the underlying mechanisms of lipid-mediated follicle development.

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