journal
https://read.qxmd.com/read/38530028/excavation-of-gene-markers-associated-with-pancreatic-ductal-adenocarcinoma-based-on-interrelationships-of-gene-expression
#1
JOURNAL ARTICLE
Zhao-Yue Zhang, Zi-Jie Sun, Dong Gao, Yu-Duo Hao, Hao Lin, Fen Liu
Pancreatic ductal adenocarcinoma (PDAC) accounts for 95% of all pancreatic cancer cases, posing grave challenges to its diagnosis and treatment. Timely diagnosis is pivotal for improving patient survival, necessitating the discovery of precise biomarkers. An innovative approach was introduced to identify gene markers for precision PDAC detection. The core idea of our method is to discover gene pairs that display consistent opposite relative expression and differential co-expression patterns between PDAC and normal samples...
March 26, 2024: IET Systems Biology
https://read.qxmd.com/read/38458989/analysis-of-disulfidptosis-and-cuproptosis-related-lncrnas-in-modulating-the-immune-microenvironment-and-chemosensitivity-in-colon-adenocarcinoma
#2
JOURNAL ARTICLE
Qiang Fan, Guang-Bo Wu, Min Chen, Lei Zheng, Hong-Jie Li, Lv-Zhu Xiang, Meng Luo
The main objective was to establish a prognostic model utilising long non-coding RNAs associated with disulfidptosis and cuproptosis. The data for RNA-Sequence and clinicopathological information of Colon adenocarcinoma (COAD) were acquired from The Cancer Genome Atlas. A prognostic model was constructed using Cox regression and the Least Absolute Shrinkage and Selection Operator method. The model's predictive ability was assessed through principal component analysis, Kaplan-Meier analysis, nomogram etc. The ability of identifying the rates of overall survival, infiltration of immune cells, and chemosensitivity was also explored...
March 8, 2024: IET Systems Biology
https://read.qxmd.com/read/38377622/anoikis-related-genes-as-potential-prognostic-biomarkers-in-gastric-cancer-a-multilevel-integrative-analysis-and-predictive-therapeutic-value
#3
JOURNAL ARTICLE
Yongjian Lin, Jinlu Liu
BACKGROUND: Gastric cancer (GC) is a frequent malignancy of the gastrointestinal tract. Exploring the potential anoikis mechanisms and pathways might facilitate GC research. PURPOSE: The authors aim to determine the significance of anoikis-related genes (ARGs) in GC prognosis and explore the regulatory mechanisms in epigenetics. METHODS: After describing the genetic and transcriptional alterations of ARGs, we searched differentially expressed genes (DEGs) from the cancer genome atlas and gene expression omnibus databases to identify major cancer marker pathways...
February 20, 2024: IET Systems Biology
https://read.qxmd.com/read/38318939/the-other-subfamily-of-hect-e3-ubiquitin-ligases-evaluate-the-tumour-immune-microenvironment-and-prognosis-in-patients-with-hepatocellular-carcinoma
#4
JOURNAL ARTICLE
Runyu Dong, Zhixiong Wang, Danping Cao, Yanna Li, Yao Fei, Peng Gao, Menglin Zhu, Zhiqiang Chen, Juan Cai, Xueliang Zuo
Primary liver cancer is the sixth most common cancer and the third leading cause of cancer-related death worldwide. The role of the 'Other' subfamily of HECT E3 ligases (E3s) in hepatocellular carcinoma (HCC) remains unknown. The expression of the 'Other' HECT E3s was performed using The Cancer Genome Atlas (TCGA) data, and the authors found that the 'Other' HECT E3s were differentially expressed in HCC. Prognostic values were assessed using the Kaplan-Meier method and indicated that the high expressions of HECTD2, HECTD3, and HACE1 were associated with a worse clinical prognosis of HCC patients...
February 6, 2024: IET Systems Biology
https://read.qxmd.com/read/38193845/machine-learning-unveils-rna-polymerase-ii-binding-as-a-predictor-for-smad2-dependent-transcription-dynamics-in-response-to-actvin-signalling
#5
JOURNAL ARTICLE
Dan Shi, Weihua Feng, Zhike Zi
The transforming growth factor-β (TGF-β) superfamily, including Nodal and Activin, plays a critical role in various cellular processes. Understanding the intricate regulation and gene expression dynamics of TGF-β signalling is of interest due to its diverse biological roles. A machine learning approach is used to predict gene expression patterns induced by Activin using features, such as histone modifications, RNA polymerase II binding, SMAD2-binding, and mRNA half-life. RNA sequencing and ChIP sequencing datasets were analysed and differentially expressed SMAD2-binding genes were identified...
January 9, 2024: IET Systems Biology
https://read.qxmd.com/read/37938890/kinetic-modelling-of-%C3%AE-cell-metabolism-reveals-control-points-in-the-insulin-regulating-pyruvate-cycling-pathways
#6
JOURNAL ARTICLE
Rahul Rahul, Adam R Stinchcombe, Jamie W Joseph, Brian Ingalls
Insulin, a key hormone in the regulation of glucose homoeostasis, is secreted by pancreatic β-cells in response to elevated glucose levels. Insulin is released in a biphasic manner in response to glucose metabolism in β-cells. The first phase of insulin secretion is triggered by an increase in the ATP:ADP ratio; the second phase occurs in response to both a rise in ATP:ADP and other key metabolic signals, including a rise in the NADPH:NADP+ ratio. Experimental evidence indicates that pyruvate-cycling pathways play an important role in the elevation of the NADPH:NADP+ ratio in response to glucose...
December 2023: IET Systems Biology
https://read.qxmd.com/read/37823415/identification-of-toll-like-receptor-5-and-acyl-coa-synthetase-long-chain-family-member-1-as-hub-genes-are-correlated-with-the-severe-forms-of-covid-19-by-weighted-gene-co-expression-network-analysis
#7
JOURNAL ARTICLE
Luoyi Wang, Zhaomin Mao, Fengmin Shao
Since a 25% mortality rate occurred in critical Coronavirus disease 2019 (COVID-19) patients, investigating the potential drivers remains to be important. Here, the authors applied Weighted Gene Co-expression Network Analysis to identify the potential drivers in the blood samples of multiple COVID-19 expression profiles. The authors found that the darkslateblue module was significantly correlated with critical COVID-19, and Gene Ontology analysis indicated terms associated with the inflammation pathway and apoptotic process...
December 2023: IET Systems Biology
https://read.qxmd.com/read/37957441/research-on-symptoms-composition-time-series-evolution-and-network-visualisation-of-interstitial-cystitis-based-on-complex-network-community-discovery-algorithm
#8
JOURNAL ARTICLE
Lei Pang, Zijun Ding, Xiaodong Bian, Weibing Shuang
We analyzed the symptoms composition of Interstitial Cystitis (IC), the regularity of the evolution of symptoms before and after treatment, and the visualization of the community network, to provide a reference for clinical diagnosis and treatment of Interstitial Cystitis. Based on the outpatient electronic case data of 552 patients with Interstitial Cystitis, we used a complex network community discovery algorithm, directed weighted complex network, and Sankey map to mine the data of the symptoms composition of Interstitial Cystitis, the evolution of symptoms before and after treatment and the visualization of the community network, to analyze the epidemiological characteristics of interstitial cystitis symptoms in the real world...
November 13, 2023: IET Systems Biology
https://read.qxmd.com/read/37935646/bioinformatics-identification-of-a-t-cell-related-signature-for-predicting-prognosis-and-drug-sensitivity-in-hepatocellular-carcinoma
#9
JOURNAL ARTICLE
Dianqian Wang, Dongxiao Ding, Junjie Ying, Yunsheng Qin
Hepatocellular carcinoma (HCC) is a fatal disease with poor clinical outcomes. T cells play a vital role in the crosstalk between the tumour microenvironment and HCC. Single-cell RNA sequencing data were downloaded from the GSE149614 dataset. The T-cell-related prognostic signature (TRPS) was developed with the integrative procedure including 10 machine learning algorithms. The TRPS was established using 7 T-cell-related markers in the Cancer Genome Atlas cohort with 1-, 2- and 3-year area under curve values of 0...
November 7, 2023: IET Systems Biology
https://read.qxmd.com/read/37907428/prediction-and-analysis-of-genetic-effect-in-idiopathic-pulmonary-fibrosis-and-gastroesophageal-reflux-disease
#10
JOURNAL ARTICLE
Peipei Chen, Lubin Xie, Leikai Ma, Xianda Zhao, Yong Chen, Zhouling Ge
With increasing research on idiopathic pulmonary fibrosis (IPF) and gastroesophageal reflux disease (GERD), more and more studies have indicated that GERD is associated with IPF, but the underlying pathological mechanisms remain unclear. The aim of the present study is to identify and analyse the differentially expressed genes (DEGs) between IPF and GERD and explore the relevant molecular mechanisms via bioinformatics analysis. Four GEO datasets (GSE24206, GSE53845, GSE26886, and GSE39491) were downloaded from the GEO database, and DEGs between IPF and GERD were identified with the online tool GEO2R...
October 31, 2023: IET Systems Biology
https://read.qxmd.com/read/37814484/bioinformatics-approach-to-identify-the-hub-gene-associated-with-covid-19-and-idiopathic-pulmonary-fibrosis
#11
JOURNAL ARTICLE
Wenchao Shi, Tinghui Li, Huiwen Li, Juan Ren, Meiyu Lv, Qi Wang, Yaowu He, Yao Yu, Lijie Liu, Shoude Jin, Hong Chen
The coronavirus disease 2019 (COVID-19) has developed into a global health crisis. Pulmonary fibrosis, as one of the complications of SARS-CoV-2 infection, deserves attention. As COVID-19 is a new clinical entity that is constantly evolving, and many aspects of disease are remain unknown. The datasets of COVID-19 and idiopathic pulmonary fibrosis were obtained from the Gene Expression Omnibus. The hub genes were screened out using the Random Forest (RF) algorithm depending on the severity of patients with COVID-19...
October 9, 2023: IET Systems Biology
https://read.qxmd.com/read/37787083/robust-positive-control-of-tumour-growth-using-angiogenic-inhibition
#12
JOURNAL ARTICLE
Mohamadreza Homayounzade, Maryam Homayounzadeh, Mohammad Hassan Khooban
In practice, many physical systems, including physiological ones, can be considered whose input can take only positive quantities. However, most of the conventional control methods do not support the positivity of the main input data to the system. Furthermore, the parameters of these systems, similar to other non-linear systems, are either not accurately identified or may change over time. Therefore, it is reasonable to design a controller that is robust against system uncertainties. A robust positive-input control method is proposed for the automatic treatment of targeted anti-angiogenic therapy implementing a recently published tumour growth model based on experiments conducted on mouse models...
October 2023: IET Systems Biology
https://read.qxmd.com/read/37776100/identification-of-basement-membrane-markers-in-diabetic-kidney-disease-and-immune-infiltration-by-using-bioinformatics-analysis-and-experimental-verification
#13
JOURNAL ARTICLE
Rui Shi, Wen-Man Zhao, Li Zhu, Rui-Feng Wang, De-Guang Wang
Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease worldwide. Basement membranes (BMs) are ubiquitous extracellular matrices which are affected in many diseases including DKD. Here, the authors aimed to identify BM-related markers in DKD and explored the immune cell infiltration in this process. The expression profiles of three datasets were downloaded from the Gene Expression Omnibus database. BM-related differentially expression genes (DEGs) were identified and Kyoto encyclopaedia of genes and genomes pathway enrichment analysis were applied to biological functions...
September 30, 2023: IET Systems Biology
https://read.qxmd.com/read/37606290/an-immune-related-multi-omics-analysis-of-dolichyl-diphosphooligosaccharide-protein-glycosyltransferase-in-glioma-prognostic-value-exploration-and-competitive-endogenous-rna-network-identification
#14
JOURNAL ARTICLE
Jie Liu, Chao Feng, Min Liu, Yan Zhou, Yuezhen Shen, Jianxin Li, Xiangyang Wei
Dolichyl-diphosphooligosaccharide protein glycosyltransferase (DDOST) plays a pivotal role in the glycosylation of asparagine residues on nascent polypeptides. However, the biological role of DDOST in glioma remains unclear. The mRNA expression of DDOST in glioma was identified using TCGA, CGGA, GEO and Rembrandt datasets. Immunohistochemistry assay was conducted to examine the protein level of DDOST. Cox regression analysis, nomograms and calibration plots were used to evaluate the prognostic value of DDOST...
August 22, 2023: IET Systems Biology
https://read.qxmd.com/read/37515398/single-cell-rna-sequencing-identifies-macrophage-signatures-correlated-with-clinical-features-and-tumour-microenvironment-in-meningiomas
#15
JOURNAL ARTICLE
Xiaowei Zhang
BACKGROUND: Meningiomas are common primary brain tumours, with macrophages playing a crucial role in their development and progression. This study aims to identify module genes correlated with meningioma-associated macrophages and analyse their correlation with clinical features and immune infiltration. METHODS: We analysed single-cell RNA sequencing (scRNA-seq) data from two paired meningioma and normal meninges to identify meningioma-associated macrophages. High-dimensional weighted gene co-expression network analysis (hdWGCNA) was employed to identify module genes linked to these macrophages, followed by functional enrichment and pseudotime trajectory analyses...
July 29, 2023: IET Systems Biology
https://read.qxmd.com/read/37488766/high-expression-of-centromere-protein-a-and-its-molecular-mechanism-and-clinical-significance-in-prostate-cancer-a-study-based-on-data-mining-and-immunohistochemistry
#16
JOURNAL ARTICLE
Fang-Cheng Jiang, Gao-Qiang Zhai, Jia-Lin Liu, Rui-Gong Wang, Yuan-Ping Yang, Harivignesh Murugesan, Xiao-Xiang Yu, Xiu-Fang Du, Juan He, Zhen-Bo Feng, Shang Ling Pan, Gang Chen, Sheng-Hua Li, Zhi-Guang Huang
The progression of prostate cancer (PCa) leads to poor prognosis. However, the molecular mechanism of PCa is still not completely clear. This study aimed to elucidate the important role of centromere protein A (CENPA) in PCa. Large numbers of bulk RNA sequencing (RNA-seq) data and in-house immunohistochemistry data were used in analysing the expression level of CENPA in PCa and metastatic PCa (MPCa). Single-cell RNA-seq data was used to explore the expression status of CENPA in different prostate subpopulations...
July 24, 2023: IET Systems Biology
https://read.qxmd.com/read/37466160/deep-sequencing-of-circulating-mirnas-and-target-mrnas-level-in-deep-venous-thrombosis-patients
#17
JOURNAL ARTICLE
Qingxian Wang, Yunhe Chang, Xuqing Yang, Ziwang Han
Deep venous thrombosis is one of the most common peripheral vascular diseases that lead to major morbidity and mortality. The authors aimed to identify potential differentially expressed miRNAs and target mRNAs, which were helpful in understanding the potential molecule mechanism of deep venous thrombosis. The plasma samples of patients with deep venous thrombosis were obtained for the RNA sequencing. Differentially expressed miRNAs were identified, followed by miRNA-mRNA target analysis. Enrichment analysis was used to analyze the potential biological function of target mRNAs...
July 19, 2023: IET Systems Biology
https://read.qxmd.com/read/37431829/a-novel-investigation-into-an-e2f-transcription-factor-related-prognostic-model-with-seven-signatures-for-colon-cancer-patients
#18
JOURNAL ARTICLE
Xiaoyong Shen, Zheng Su, Yan Dou, Xin Song
The pathogenesis of colon cancer, a common gastrointestinal tumour, involves complicated factors, especially a series of cell cycle-related genes. E2F transcription factors during the cell cycle play an essential role in the occurrence of colon cancer. It is meaningful to establish an efficient prognostic model of colon cancer targeting cellular E2F-associated genes. This has not been reported previously. The authors first aimed to explore the links of E2F genes with the clinical outcomes of colon cancer patients by integrating data from the TCGA-COAD (n = 521), GSE17536 (n = 177) and GSE39582 (n = 585) cohorts...
July 11, 2023: IET Systems Biology
https://read.qxmd.com/read/37431788/single-cell-rna-seq-and-bulk-rna-seq-explore-the-prognostic-value-of-exhausted-t-cells-in-hepatocellular-carcinoma
#19
JOURNAL ARTICLE
Xiaolong Tang, Yandong Miao, Lixia Yang, Wuhua Ha, Zheng Li, Denghai Mi
Hepatocellular carcinoma (HCC) remains a worldwide health problem. Mounting evidence indicates that exhausted T cells play a critical role in the progress and treatment of HCC. Therefore, a detailed characterisation of exhausted T cells and their clinical significance warrants further investigation in HCC. Based on the GSE146115, we presented a comprehensive single-cell Atlas in HCC. Pseudo-time analysis revealed that tumour heterogeneity progressively increased, and the exhausted T cells gradually appeared during tumour progression...
July 11, 2023: IET Systems Biology
https://read.qxmd.com/read/37417684/comprehensive-analysis-of-anoikis-related-lncrnas-for-predicting-prognosis-and-response-of-immunotherapy-in-hepatocellular-carcinoma
#20
JOURNAL ARTICLE
Sihao Du, Ke Cao, Zhenshun Wang, Dongdong Lin
Nowadays, primary liver cancer is still a major threat to human health. Anoikis is a particular form of programed cell death that has an inhibitory effect on neoplasm metastasis. Although several prognostic models based on anoikis-related genes for Hepatocellular carcinoma (HCC) have been established, signatures associated with anoikis-related lncRNAs have not been identified. To fill this blank space, the authors built up a prognostic signature and appraised its value in guiding immunotherapy. Eleven prognostic anoikis-related lncRNAs were identified through Least Absolute Shrinkage and Selection Operator Cox analysis...
July 7, 2023: IET Systems Biology
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