Gene Ontology and KEGG Pathway Enrichment Analysis of a Drug Target-Based Classification System

Microorganism is an important part of ecosystems; it is very sensitive to environmental change. In order to study the effects of sound on organisms, it’s meaningful to study mechanism of microbial exposure to sound. In our previous experiments, the effects of different sound intensity and frequency on the growth of E. coli K12 were studied. It was found that in stationary phase the bacteria concentration of sound expose group was higher than control. In this study, we aimed to understand the mechanisms of E. coli underlying sound expose by using Gene Ontology and KEGG Pathway Enrichment Analysis, and established a systematic pathway for the E. coli response to sound expose. At 6 hour, the chemotaxis pathway was significantly up-regulated which responses to the changes of the external environment and leads bacteria to favorable environment. At 12 hour, the glycerophospholipid pathway was significant up-regulated, it is related to the energy metabolism and cell division. At 24 hours, the energy metabolism, nucleotide synthesis and transcriptional translation pathways were significant differences. When bacteria entered the stationary phase (36 hour), in sound exposure group the pathways related to reduce the harmful substances were down-regulated and the pathways about degrade aromatic compounds provides energy were up-regulated, so that the E. coli K12 in sound exposure have a better ability to adapt poor living environment. Comparative transcriptome analysis of sound exposed E. coli K12 can not only reveal the behavior of E. coli K12 response to sound expose, but also lay a foundation for further study the mechanism of prokaryotes response to physical stimulus.

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The influence of metabolic network structures and energy metabolic pattern on E. coli K12 exposed to acoustic field: based on Gene Ontology and KEGG pathway enrichment analysis

10.7287/peerj.preprints.2821v1 ◽

2017 ◽

Cited By ~ 1

Author(s):

Shaobin Gu ◽

Suyu Qiao ◽

Ying Wu

Keyword(s):

Gene Ontology ◽

Energy Metabolism ◽

Stationary Phase ◽

Kegg Pathway ◽

Enrichment Analysis ◽

Living Environment ◽

Pathway Enrichment Analysis ◽

E Coli ◽

Pathway Enrichment ◽

Sound Exposure

Microorganism is an important part of ecosystems; it is very sensitive to environmental change. In order to study the effects of sound on organisms, it’s meaningful to study mechanism of microbial exposure to sound. In our previous experiments, the effects of different sound intensity and frequency on the growth of E. coli K12 were studied. It was found that in stationary phase the bacteria concentration of sound expose group was higher than control. In this study, we aimed to understand the mechanisms of E. coli underlying sound expose by using Gene Ontology and KEGG Pathway Enrichment Analysis, and established a systematic pathway for the E. coli response to sound expose. At 6 hour, the chemotaxis pathway was significantly up-regulated which responses to the changes of the external environment and leads bacteria to favorable environment. At 12 hour, the glycerophospholipid pathway was significant up-regulated, it is related to the energy metabolism and cell division. At 24 hours, the energy metabolism, nucleotide synthesis and transcriptional translation pathways were significant differences. When bacteria entered the stationary phase (36 hour), in sound exposure group the pathways related to reduce the harmful substances were down-regulated and the pathways about degrade aromatic compounds provides energy were up-regulated, so that the E. coli K12 in sound exposure have a better ability to adapt poor living environment. Comparative transcriptome analysis of sound exposed E. coli K12 can not only reveal the behavior of E. coli K12 response to sound expose, but also lay a foundation for further study the mechanism of prokaryotes response to physical stimulus.

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

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207322666190717124507 ◽

2019 ◽

Vol 22 (6) ◽

pp. 411-420 ◽

Cited By ~ 5

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.

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System Pharmacological Mechanism and Compatibility Laws of Jianghuang from Traditional Chinese Medicine In Blood-Regulating Formulae

10.21203/rs.3.rs-29958/v1 ◽

2020 ◽

Author(s):

Zhiqiang Liu ◽

Bolong Wang

Keyword(s):

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Kegg Pathway ◽

Inflammatory Diseases ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Pharmacological Effects ◽

Ppi Network ◽

Pathway Enrichment ◽

Pharmacological Mechanism

Abstract Background: Jianghuang (JH) is a popular ingredient in blood-regulating traditional Chinese Medicine (TCM) that could be effective for the treatment of various diseases. We demonstrate the compatibility laws and system pharmacological mechanisms of the key formula containing JH by leveraging data mining of bioinformatics databases.Material/Methods: The compatibility laws of blood-regulating formulae containing JH from the Chinese Traditional Medicine Formula Dictionary were analyzed using a generalized rule induction (GRI) algorithm implemented. The putative target gene and miRNA were retrieved via a combination of the Arrowsmith knowledge discovery tool and FunRich 3.1.3. System pharmacological mechanisms are traced by their protein-protein interaction (PPI) network, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted using Uniprot, the Human Protein Atlas (HPA), STRING 11.0, and KOBAS 3.0.Results: We found that the JH-CX-DG formula (Ligusticum chuanxiong-Angelica sinensis) could represent a key formula containing JH in blood-regulating TCM formulae. The JH-CX-DG formula was observed to directly target AKT, TLR4, caspase-3, PI3K, mTOR, p38 MAPK, VEGF, iNOS, Nrf2, BDNF, NF-κB, Bcl-2, and Bax 13 targets and regulate targets through 13 miRNA. The PPI network and KEGG pathway enrichment analysis showed that the JH-CX-DG formula possess potential pharmacological effects including anti-inflammatory, improving microcirculation, and anti-tumor through the regulation of multiple pathways including PI3K/Akt, MAPK, Toll-like receptor, T cell receptor, EGFR, VEGFR, Apoptosis, HIF-1 (p < 0.05).Conclusion: The JH-CX-DG formula can exert beneficial pharmacological effects through multi-target and multi-pathway interactions. It can be effectively administered for the treatment of inflammatory diseases, microcirculation disorders, cardiovascular disease, and cancer. We found a new effective drug formula through analyzing the compatibility law and systemic pharmacological mechanism of JH. Our study provides a theoretical basis and directions for subsequent research on the JH-CX-DG formula.

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

Scientific Reports ◽

10.1038/s41598-020-78191-8 ◽

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.

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Serum MiR-4687-3p Has Potential for Diagnosis and Carcinogenesis in Non-small Cell Lung Cancer

Frontiers in Genetics ◽

10.3389/fgene.2020.597508 ◽

2020 ◽

Vol 11 ◽

Author(s):

Man Liu ◽

Qiufang Si ◽

Songyun Ouyang ◽

Zhigang Zhou ◽

Meng Wang ◽

...

Keyword(s):

Lung Cancer ◽

Validation Cohort ◽

Kegg Pathway ◽

Enrichment Analysis ◽

Small Cell ◽

Pathway Enrichment Analysis ◽

Small Cell Lung ◽

Invasion And Migration ◽

Pathway Enrichment ◽

And Migration

The lack of a useful biomarker partly contributes to the increased mortality of non-small cell lung cancer (NSCLC). MiRNAs have become increasingly appreciated in diagnosis of NSCLC. In the present study, we used microarray to screen 2,549 miRNAs in serum samples from the training cohort (NSCLC, n = 10; the healthy, n = 10) to discover differentially expressed miRNAs (DEMs). Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) assay was applied to validate the expression level of selected overexpressed DEMs of NSCLC in a validation cohort (NSCLC, n = 30; the healthy, n = 30). Area under the receiver operating characteristic curve (AUC) was performed to evaluate diagnostic capability of the DEMs. The expression of the miRNAs in tissues was analyzed based on the TCGA database. Subsequently, the target genes of the miR-4687-3p were predicted by TargetScan. Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were tested by R software (ClusterProfiler package). NSCLC cells were transfected with inhibitor or mimic to down-regulate or up-regulate the miR-4687-3p level. The function of miR-4687-3p on proliferation, invasion, and migration of lung cancer cells were investigated through CCK-8 and Transwell assays, respectively. In the results, we identified serum miR-4687-3p that provided a high diagnostic accuracy of NSCLC (AUC = 0.679, 95%CI: 0.543–0.815) in the validation cohort. According to the TCGA database, we found that the miR-4687-3p level was significantly higher in NSCLC tissues than in normal lung tissues (p < 0.05). GO and KEGG pathway enrichment analysis showed that postsynaptic specialization and TGF-β signaling pathway were significantly enriched. Down-regulation of miR-4687-3p could suppress the proliferation, invasion, and migration of the NSCLC cells, compared with inhibitor negative control (NC). Meanwhile, overexpression of miR-4687-3p could promote the proliferation, invasion, and migration of the NSCLC cells compared with mimic NC. As a conclusion, our study first discovered that serum miR-4687-3p might have clinical potential as a non-invasive diagnostic biomarker for NSCLC and play an important role in the development of NSCLC.

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Potential Targets and Clinical Value of MiR-224-5p in Cancers of the Digestive Tract

Cellular Physiology and Biochemistry ◽

10.1159/000485281 ◽

2017 ◽

Vol 44 (2) ◽

pp. 682-700 ◽

Cited By ~ 8

Author(s):

Lu Zhang ◽

Lan-shan Huang ◽

Gang Chen ◽

Zhen-bo Feng

Keyword(s):

Digestive Tract ◽

Digestive System ◽

Kegg Pathway ◽

Univariate Analysis ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Clinical Value ◽

Go Annotation ◽

Pathway Enrichment ◽

Target Mrnas

Background/Aims: MicroRNAs participate in various biological processes in malignant tumors. However, the mechanisms of miR-224-5p in digestive system cancers are not fully understood. A comprehensive investigation of the clinical value and potential targets of miR-224-5p in cancers of the digestive tract is necessary. Methods: Expression profiling data and related-prognostic data of miR-224-5p were acquired from Gene Expression Omnibus, The Cancer Genome Atlas, ArrayExpress, and published literature. The potential target mRNAs of miR-224-5p were predicted using bioinformatics methods and finally annotated using Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Results: MiR-224-5p is up-regulated in digestive system cancers (SMD=0.69, 95% CI: 0.43-0.96, P<0.0001) and exhibits a moderate diagnostic ability (AUC=0.84, 95% CI: 0.80-0.87). Our data also demonstrated that miR-224-5p is statistically significantly correlated with overall survival univariate analysis (HR=1.69, 95% CI: 1.15-2.49, P=0.007) and multivariate analysis (HR=2.39, 95% CI: 1.74-3.30, P<0.0001). In total, 388 potential miR-224-5p target mRNAs were predicted by bioinformatics methods. GO annotation analysis revealed that the top terms of miR-224-5p in biological process, cellular component and molecular function were system development, neuron part, and transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding, respectively. Moreover, eight pathways were identified in KEGG pathway enrichment analysis. Conclusions: MiR-224-5p is up-regulated and has the potential to become a diagnostic and prognostic biomarker in digestive system cancers. MiR-224-5p might play vital roles in cancers of the digestive tract but the exact molecular mechanisms need further study and verification.

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UBE2T Contributes to the Prognosis of Esophageal Squamous Cell Carcinoma

Pathology & Oncology Research ◽

10.3389/pore.2021.632531 ◽

2021 ◽

Vol 27 ◽

Author(s):

Xiaoyuan Wang ◽

Yang Liu ◽

Xue Leng ◽

Kui Cao ◽

Wentao Sun ◽

...

Keyword(s):

High Risk ◽

Squamous Cell ◽

Kegg Pathway ◽

Risk Group ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Cox Regression Analysis ◽

Gene Signatures ◽

Pathway Enrichment

Background: The ubiquitin-conjugating enzyme E2 T (UBE2T) has been shown to contribute to several types of cancer. However, no publication has reported its implication in esophageal squamous cell cancer (ESCC).Methods: We explored several public databases, including The Cancer Genome Atlas (TCGA), Oncomine, and gene expression Omnibus (GEO). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene set enrichment analysis (GSEA) were adopted to explore involved signaling pathways. We used R software to develop prognostic gene signatures with the LASSO and stepwise Cox regression analysis, separately. Immunohistochemistry staining was performed to detect UBE2T in 90 ESCC patients, followed by survival analysis. We also used an R package pRRophetic to evaluate chemotherapy sensitivity for the TCGA–ESCC cohort.Results: We found significantly increased UBE2T transcript levels and DNA copy numbers in ESCC tissues. UBE2T was associated with the p53 signaling pathway, cell cycle, Fanconi anemia pathway, and DNA replication, as indicated by Go, KEGG pathway enrichment analysis. These pathways were also upregulated in ESCC. The prognostic signatures with UBE2T-associated genes could stratify ESCC patients into low- and high-risk groups with significantly different overall survival in the TCGA–ESCC cohort. We also validated the association of UBE2T with unfavorable survival in 90 ESCC patients recruited for this study. Moreover, we found that the low-risk group was significantly more sensitive to chemotherapy than the high-risk group.Conclusions: UBE2T is involved in the development of ESCC, and gene signatures derived from UBE2T-associated genes are predictive of prognosis in ESCC.

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Quantitative Phosphoproteomic Comparison of Lens Proteins in Highly Myopic Cataract and Age-Related Cataract

BioMed Research International ◽

10.1155/2021/6668845 ◽

2021 ◽

Vol 2021 ◽

pp. 1-18

Author(s):

Shaohua Zhang ◽

Keke Zhang ◽

Wenwen He ◽

Yi Lu ◽

Xiangjia Zhu

Keyword(s):

Molecular Mechanisms ◽

Kegg Pathway ◽

Phosphoglycerate Kinase ◽

Enrichment Analysis ◽

Glutathione Metabolism ◽

Pathway Enrichment Analysis ◽

Phosphorylation Sites ◽

Pathway Enrichment ◽

Age Related ◽

Go Enrichment

Purpose. To investigate and compare the lens phosphoproteomes in patients with highly myopic cataract (HMC) or age-related cataract (ARC). Methods. In this study, we undertook a comparative phosphoproteome analysis of the lenses from patients with HMC or ARC. Intact lenses from ARC and HMC patients were separated into the cortex and nucleus. After protein digestion, the phosphopeptides were quantitatively analyzed with TiO2 enrichment and liquid chromatography-mass spectrometry. The potential functions of different phosphopeptides were assessed by Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Results. In total, 522 phosphorylation sites in 164 phosphoproteins were identified. The number of phosphorylation sites was significantly higher in the cortex than in the nucleus, in both ARC and HMC lenses. The differentially phosphorylated peptides in the lens cortex and nucleus in HMC eyes were significantly involved in the glutathione metabolism pathway. The KEGG pathway enrichment analysis indicated that the differences in phosphosignaling mediators between the ARC and HMC lenses were associated with glycolysis and the level of phosphorylated phosphoglycerate kinase 1 was lower in HMC lenses than in ARC lenses. Conclusions. We provide an overview of the differential phosphoproteomes of HMC and ARC lenses that can be used to clarify the molecular mechanisms underlying their different phenotypes.

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

10.7287/peerj.preprints.3336v1 ◽

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.

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