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Research on symptoms composition, time series evolution, and network visualisation of interstitial cystitis based on complex network community discovery algorithm. IET Syst. Biol. (IF 2.3) Pub Date : 2023-11-13 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
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Bioinformatics identification of a T-cell-related signature for predicting prognosis and drug sensitivity in hepatocellular carcinoma. IET Syst. Biol. (IF 2.3) Pub Date : 2023-11-07 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
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Prediction and analysis of genetic effect in idiopathic pulmonary fibrosis and gastroesophageal reflux disease. IET Syst. Biol. (IF 2.3) Pub Date : 2023-10-31 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
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Bioinformatics approach to identify the hub gene associated with COVID-19 and idiopathic pulmonary fibrosis. IET Syst. Biol. (IF 2.3) Pub Date : 2023-10-09 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
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Robust positive control of tumour growth using angiogenic inhibition. IET Syst. Biol. (IF 2.3) Pub Date : 2023-10-03 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
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Identification of basement membrane markers in diabetic kidney disease and immune infiltration by using bioinformatics analysis and experimental verification. IET Syst. Biol. (IF 2.3) Pub Date : 2023-09-30 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
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An immune-related multi-omics analysis of dolichyl-diphosphooligosaccharide protein glycosyltransferase in glioma: Prognostic value exploration and competitive endogenous RNA network identification. IET Syst. Biol. (IF 2.3) Pub Date : 2023-08-22 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
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Single-cell RNA sequencing identifies macrophage signatures correlated with clinical features and tumour microenvironment in meningiomas. IET Syst. Biol. (IF 2.3) Pub Date : 2023-07-29 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
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High expression of centromere protein A and its molecular mechanism and clinical significance in prostate cancer: A study based on data mining and immunohistochemistry. IET Syst. Biol. (IF 2.3) Pub Date : 2023-07-24 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)
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Deep sequencing of circulating miRNAs and target mRNAs level in deep venous thrombosis patients. IET Syst. Biol. (IF 2.3) Pub Date : 2023-07-19 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
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A novel investigation into an E2F transcription factor-related prognostic model with seven signatures for colon cancer patients. IET Syst. Biol. (IF 2.3) Pub Date : 2023-07-11 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
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Single-cell RNA-seq and bulk RNA-seq explore the prognostic value of exhausted T cells in hepatocellular carcinoma. IET Syst. Biol. (IF 2.3) Pub Date : 2023-07-11 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
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Comprehensive analysis of anoikis-related lncRNAs for predicting prognosis and response of immunotherapy in hepatocellular carcinoma. IET Syst. Biol. (IF 2.3) Pub Date : 2023-07-07 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
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Cuproptosis-related lncRNAs are correlated with tumour metabolism and immune microenvironment and predict prognosis in pancreatic cancer patients. IET Syst. Biol. (IF 2.3) Pub Date : 2023-06-21 Yanling Wang,Weiyu Ge,Shengbai Xue,Jiujie Cui,Xiaofei Zhang,Tiebo Mao,Haiyan Xu,Shumin Li,Jingyu Ma,Ming Yue,Daiyuan Shentu,Liwei Wang
Cuproptosis is a novel cell death pathway, and the regulatory mechanism in pancreatic cancer (PC) is unclear. The authors aimed to figure out whether cuproptosis-related lncRNAs (CRLs) could predict prognosis in PC and the underlying mechanism. First, the prognostic model based on seven CRLs screened by the least absolute shrinkage and selection operator Cox analysis was constructed. Following this
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A comprehensive analysis of FBN2 in bladder cancer: A risk factor and the tumour microenvironment influencer. IET Syst. Biol. (IF 2.3) Pub Date : 2023-06-19 Zechao Lu,Zeguang Lu,Yongchang Lai,Haobin Zhou,Zhibiao Li,Wanyan Cai,Zeyao Xu,Hongcheng Luo,Yushu Chen,Jianyu Li,Jishen Zhang,Zhaohui He,Fucai Tang
Bladder cancer (BLCA) is a common and difficult-to-manage disease worldwide. Most common type of BLCA is urothelial carcinoma (UC). Fibrillin 2 (FBN2) was first discovered while studying Marfan syndrome, and its encoded products are associated with elastin fibres. To date, the role of FBN2 in BLCA remains unclear. The authors first downloaded data from The Cancer Genome Atlas (TCGA) and Gene Expression
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Identification of genomic biomarkers and their pathway crosstalks for deciphering mechanistic links in glioblastoma. IET Syst. Biol. (IF 2.3) Pub Date : 2023-06-05 Darrak Moin Quddusi,Naim Bajcinca
Glioblastoma is a grade IV pernicious neoplasm occurring in the supratentorial region of brain. As its causes are largely unknown, it is essential to understand its dynamics at the molecular level. This necessitates the identification of better diagnostic and prognostic molecular candidates. Blood-based liquid biopsies are emerging as a novel tool for cancer biomarker discovery, guiding the treatment
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Hub genes and pathways in gastric cancer: A comparison between studies that used normal tissues adjacent to the tumour and studies that used healthy tissues as calibrator. IET Syst. Biol. (IF 2.3) Pub Date : 2023-04-29 Khadijeh Sadegh,Amirhossein Ahmadi
Several bioinformatics studies have been performed on high-throughput expression data to determine the cellular pathways and hub genes affected by Gastric cancer (GC). However, these studies differ in using a healthy tissue or normal tissue adjacent to the tumour (NAT) as calibrator tissues. This study was designed to find how using healthy or NAT tissues as calibrator tissues could affect pathway
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Chromosome instability-associated prognostic signature and cluster investigation for cutaneous melanoma cases. IET Syst. Biol. (IF 2.3) Pub Date : 2023-04-25 Ning Liu,Guangjing Liu,Qian Ma,Xiaobing Li
Chromosomal instability (CIN) is closely associated to the early detection of several clinical tumours. In this study, the authors first established a novel prognostic model of melanoma using the hub genes of CIN, based on the datasets of The cancer genome atlas-skin cutaneous melanoma (TCGA-SKCM) and GSE65904 cohorts. Based on the risk scores of our model, the disease-specific survival (DSS) prognosis
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Fusion of various optimisation based feature smoothing methods for wearable and non-invasive blood glucose estimation. IET Syst. Biol. (IF 2.3) Pub Date : 2023-03-31 Yiting Wei,Bingo Wing-Kuen Ling,Danni Chen,Yuheng Dai,Qing Liu
The traditional blood glucose estimation method requires to take the invasive measurements several times a day. Therefore, it has a high infection risk and the users are suffered from the pain. Moreover, the long term consumable cost is high. Recently, the wearable and non-invasive blood glucose estimation approach has been proposed. However, due to the unreliability of the acquisition device, the
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Identification of key immune-related genes and immune infiltration in diabetic nephropathy based on machine learning algorithms. IET Syst. Biol. (IF 2.3) Pub Date : 2023-03-14 Yue Sun,Weiran Dai,Wenwen He
BACKGROUND Diabetic nephropathy (DN) is a complication of diabetes. This study aimed to identify potential diagnostic markers of DN and explore the significance of immune cell infiltration in this pathology. METHODS The GSE30528, GSE96804, and GSE1009 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified by merging the GSE30528 and
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In silico analysis of the association between long non-coding RNA family with sequence similarity 99 member A (FAM99A) and hepatic cancer. IET Syst. Biol. (IF 2.3) Pub Date : 2023-02-28 Manyi Sun,Shuhua Lv,Jin Zhong
The link between family with sequence similarity 99 member A (FAM99A), a type of long non-coding RNA, and tumourigenesis remains ambiguous. Therefore, in this study, the authors conducted an expression profile analysis of FAM99A based on 33 types of cancer within The Cancer Genome Atlas project. The expression profile data revealed low expression levels of FAM99A in hepatocellular carcinoma, cholangiocarcinoma
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Down-regulation and clinical significance of Sorbin and SH3 domain-containing protein 1 in bladder cancer tissues. IET Syst. Biol. (IF 2.3) Pub Date : 2023-02-28 Sheng-Hua Li,Gao-Qiang Zhai,Rong-Quan He,Gang Chen,Shi-Shuo Wang,Jia-Lin Liu,Ji-Wen Cheng,Hai-Biao Yan,Zhi-Guang Huang
Bladder cancer (BC) is a common cancer worldwide with a high prevalence. This study was conducted to elucidate the expression and clinical significance of Sorbin and SH3 domain-containing protein 1 (SORBS1) in BC as well as to explore its molecular mechanism in BC tumourigenesis. RNA-sequencing data, microarray, and Immunohistochemistry (IHC) were applied to elucidated the SORBS1 expression at multiple
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Identification of molecular subtypes of ischaemic stroke based on immune-related genes and weighted co-expression network analysis. IET Syst. Biol. (IF 2.3) Pub Date : 2023-02-18 Duncan Wei,Xiaopu Chen,Jing Xu,Wenzhen He
Immune system has been reported to play a key role in the development of ischaemic stroke (IS). Nevertheless, its exact immune-related mechanism has not yet been fully revealed. Gene expression data of IS and healthy control samples was downloaded from Gene Expression Omnibus database and differentially expressed genes (DEGs) was obtained. Immune-related genes (IRGs) data was downloaded from the ImmPort
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Comprehensive analysis of LILR family genes expression and tumour-infiltrating immune cells in early-stage pancreatic ductal adenocarcinoma. IET Syst. Biol. (IF 2.3) Pub Date : 2023-02-07 Qiang Gao,Shutian Mo,Chuangye Han,Xiwen Liao,Chengkun Yang,Xiangkun Wang,Tianyi Liang,Yongfei He,Zijun Chen,Guangzhi Zhu,Hao Su,Xinping Ye,Tao Peng
Leucocyte immunoglobulin-like receptors (LILRs) are closely related to tumourigenesis, but their clinical value in early-stage pancreatic ductal adenocarcinoma (PDAC) after pancreaticoduodenectomy remains unknown. Kaplan-Meier and Cox proportional hazards regression models is used to investigate the association between LILR expression and prognosis in tumour biopsies and peripheral blood mononuclear
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Development and validation of an immune-related gene signature for prognosis in Lung adenocarcinoma. IET Syst. Biol. (IF 2.3) Pub Date : 2023-02-02 Zehuai Guo,Xiangjun Qi,Zeyun Li,Jianying Yang,Zhe Sun,Peiqin Li,Ming Chen,Yang Cao
The most common type of lung cancer tissue is lung adenocarcinoma. The TCGA-LUAD cohort retrieved from the TCGA dataset was considered the internal training cohort, while GSE68465 and GSE13213 datasets from the GEO database were used as the external test cohort. The TCGA-LUAD cohort was classified into two immune subtypes using single-sample gene set enrichment analysis of the immune gene set and unsupervised
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Comprehensive analysis of alternative splicing signatures in pancreatic head cancer. IET Syst. Biol. (IF 2.3) Pub Date : 2022-12-07 Lingshan Zhou,Yuan Yang,Jian Ma,Min Liu,Rong Liu,Xiaopeng Ma,Chengdong Qiao
The correlation between dysregulation of splicing and cancers has been increasingly recognised and confirmed. The identification of valuable alternative splicing (AS) in pancreatic head cancer (PHC) has a great significance. AS profiles in PHC were generated using the data from The Cancer Genome Atlas and TCGASpliceSeq. Then, the NMF clustering method was performed to identify overall survival-associated
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The effect of normalisation and error model choice on the distribution of the maximum likelihood estimator for a biochemical reaction. IET Syst. Biol. (IF 2.3) Pub Date : 2022-11-28 Caterina Thomaseth,Nicole E Radde
Sparse and noisy measurements make parameter estimation for biochemical reaction networks difficult and might lead to ill-posed optimisation problems. This is potentiated if the data has to be normalised, and only fold changes rather than absolute amounts are available. Here, the authors consider the propagation of measurement noise to the distribution of the maximum likelihood (ML) estimator in an
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Genes associated with diagnosis and prognosis of Burkitt lymphoma. IET Syst. Biol. (IF 2.3) Pub Date : 2022-11-10 Albert Doughan,Samson Pandam Salifu
Burkitt lymphoma (BL) is one of the most aggressive forms of non-Hodgkin's lymphomas that affect children and young adults. The expression of genes and other molecular markers during carcinogenesis can be the basis for diagnosis, prognosis and the design of new and effective drugs for the management of cancers. The aim of this study was to identify genes that can serve as prognostic and therapeutic
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Design and implementation of an adaptive fuzzy sliding mode controller for drug delivery in treatment of vascular cancer tumours and its optimisation using genetic algorithm tool. IET Syst. Biol. (IF 2.3) Pub Date : 2022-09-30 Ehsan Sadeghi Ghasemabad,Iman Zamani,Hami Tourajizadeh,Mahdi Mirhadi,Zahra Goorkani Zarandi
In this paper, the side effects of drug therapy in the process of cancer treatment are reduced by designing two optimal non-linear controllers. The related gains of the designed controllers are optimised using genetic algorithm and simultaneously are adapted by employing the Fuzzy scheduling method. The cancer dynamic model is extracted with five differential equations, including normal cells, endothelial
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Identifying driver modules based on multi-omics biological networks in prostate cancer. IET Syst. Biol. (IF 2.3) Pub Date : 2022-08-30 Zhongli Chen,Biting Liang,Yingfu Wu,Haoru Zhou,Yuchen Wang,Hao Wu
The development of sequencing technology has promoted the expansion of cancer genome data. It is necessary to identify the pathogenesis of cancer at the molecular level and explore reliable treatment methods and precise drug targets in cancer by identifying carcinogenic functional modules in massive multi-omics data. However, there are still limitations to identifying carcinogenic driver modules by
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CHAC1 as a novel biomarker for distinguishing alopecia from other dermatological diseases and determining its severity. IET Syst. Biol. (IF 2.3) Pub Date : 2022-08-18 Hassan Karami,Samira Nomiri,Mohammad Ghasemigol,Niloufar Mehrvarzian,Afshin Derakhshani,Mohammad Fereidouni,Masoud Mirimoghaddam,Hossein Safarpour
Alopecia Areata (AA) is characterised by an autoimmune response to hair follicles (HFs) and its exact pathobiology remains unclear. The current study aims to look into the molecular changes in the skin of AA patients as well as the potential underlying molecular mechanisms of AA in order to identify potential candidates for early detection and treatment of AA. We applied Weighted Gene Co-expression
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Deep learning-based microarray cancer classification and ensemble gene selection approach. IET Syst. Biol. (IF 2.3) Pub Date : 2022-07-04 Khosro Rezaee,Gwanggil Jeon,Mohammad R Khosravi,Hani H Attar,Alireza Sabzevari
Malignancies and diseases of various genetic origins can be diagnosed and classified with microarray data. There are many obstacles to overcome due to the large size of the gene and the small number of samples in the microarray. A combination strategy for gene expression in a variety of diseases is described in this paper, consisting of two steps: identifying the most effective genes via soft ensembling
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Identification of TNFAIP6 as a hub gene associated with the progression of glioblastoma by weighted gene co-expression network analysis. IET Syst. Biol. (IF 2.3) Pub Date : 2022-06-29 Dongdong Lin,Wei Li,Nu Zhang,Ming Cai
This study aims to discover the genetic modules that distinguish glioblastoma multiforme (GBM) from low-grade glioma (LGG) and identify hub genes. A co-expression network is constructed using the expression profiles of 28 GBM and LGG patients from the Gene Expression Omnibus database. The authors performed gene ontology (GO) and Kyoto encyclopaedia of genes and genomes (KEGG) analysis on these genes
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Dynamic changes of serum cytokines in acute paraquat poisoning and changes in patients' immune function. IET Syst. Biol. (IF 2.3) Pub Date : 2022-06-27 Huimin Yuan,Qian Liu,Yulan Yu
Acute paraquat poisoning is due to the extremely severe toxicity of paraquat. After paraquat enters the human body, it will cause rapid changes in the human body system. Since paraquat poisoning will quickly invade the organs of the whole body, it may cause damage to the functions of multiple organs in the poisoned patient. The liver organ is the most important detoxification site for the human body
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Disrupted myelination network in the cingulate cortex of Parkinson's disease. IET Syst. Biol. (IF 2.3) Pub Date : 2022-04-08 Song Xie,Jiajun Yang,Shenghui Huang,Yuanlan Fan,Tao Xu,Jiangshuang He,Jiahao Guo,Xiang Ji,Zhibo Wang,Peijun Li,Jiangfan Chen,Yi Zhang
The cingulate cortex is part of the conserved limbic system, which is considered as a hub of emotional and cognitive control. Accumulating evidence suggested that involvement of the cingulate cortex is significant for cognitive impairment of Parkinson's disease (PD). However, mechanistic studies of the cingulate cortex in PD pathogenesis are limited. Here, transcriptomic and regulatory network analyses
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SRAS-net: Low-resolution chromosome image classification based on deep learning. IET Syst. Biol. (IF 2.3) Pub Date : 2022-04-04 Xiangbin Liu,Lijun Fu,Jerry Chun-Wei Lin,Shuai Liu
Prenatal karyotype diagnosis is important to determine if the foetus has genetic diseases and some congenital diseases. Chromosome classification is an important part of karyotype analysis, and the task is tedious and lengthy. Chromosome classification methods based on deep learning have achieved good results, but if the quality of the chromosome image is not high, these methods cannot learn image
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Identification and validation of a seven-gene prognostic marker in colon cancer based on single-cell transcriptome analysis. IET Syst. Biol. (IF 2.3) Pub Date : 2022-04-01 Yang Zhou,Yang Guo,Yuanhe Wang
Colon cancer (CC) is one of the most commonly diagnosed tumours worldwide. Single-cell RNA sequencing (scRNA-seq) can accurately reflect the heterogeneity within and between tumour cells and identify important genes associated with cancer development and growth. In this study, scRNA-seq was used to identify reliable prognostic biomarkers in CC. ScRNA-seq data of CC before and after 5-fluorouracil treatment
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Construction and validation of m6 A RNA methylation regulators associated prognostic model for gastrointestinal cancer. IET Syst. Biol. (IF 2.3) Pub Date : 2022-02-17 Yandong Miao,Bin Su,Xiaolong Tang,Jiangtao Wang,Wuxia Quan,Yonggang Chen,Denghai Mi
N6-methyladenosine (m6 A) RNA methylation is correlated with carcinogenesis and dynamically possessed through the m6 A RNA methylation regulators. This paper aimed to explore 13 m6 A RNA methylation regulators' role in gastrointestinal cancer (GIC) and determine the risk model and prognosis value of m6 A RNA methylation regulators in GIC. We used several bioinformatics methods to identify the differential
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RYR2 mutation in non-small cell lung cancer prolongs survival via down-regulation of DKK1 and up-regulation of GS1-115G20.1: A weighted gene Co-expression network analysis and risk prognostic models. IET Syst. Biol. (IF 2.3) Pub Date : 2021-12-07 Wenjun Ren,Yongwu Li,Xi Chen,Sheng Hu,Wanli Cheng,Yu Cao,Jingcheng Gao,Xia Chen,Da Xiong,Hongrong Li,Ping Wang
RYR2 mutation is clinically frequent in non-small cell lung cancer (NSCLC) with its function being elusive. We downloaded lung squamous cell carcinoma and lung adenocarcinoma samples from the TCGA database, split the samples into RYR2 mutant group (n = 337) and RYR2 wild group (n = 634), and established Kaplan-Meier curves. The results showed that RYR2 mutant group lived longer than the wild group
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Identification of the key genes and immune infiltrating cells determined by sex differences in ischaemic stroke through co-expression network module. IET Syst. Biol. (IF 2.3) Pub Date : 2021-11-18 Haipeng Xu,Yanzhi Ge,Yang Liu,Yang Zheng,Rong Hu,Conglin Ren,Qianqian Liu
Stroke is one of the leading causes of patients' death and long-term disability worldwide, and ischaemic stroke (IS) accounts for nearly 80% of all strokes. Differential genes and weighted gene co-expression network analysis (WGCNA) in male and female patients with IS were compared. The authors used cell type identification by estimating relative subsets of RNA transcripts (CIBERSORT) to analyse the
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PPDTS: Predicting potential drug-target interactions based on network similarity. IET Syst. Biol. (IF 2.3) Pub Date : 2021-11-16 Wei Wang,Yongqing Wang,Yu Zhang,Dong Liu,Hongjun Zhang,Xianfang Wang
Identification of drug-target interactions (DTIs) has great practical importance in the drug discovery process for known diseases. However, only a small proportion of DTIs in these databases has been verified experimentally, and the computational methods for predicting the interactions remain challenging. As a result, some effective computational models have become increasingly popular for predicting
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A novel m6A-related prognostic signature for predicting the overall survival of hepatocellular carcinoma patients. IET Syst. Biol. (IF 2.3) Pub Date : 2021-10-14 Shiyang Xie,Yaxuan Wang,Jin Huang,Guang Li
Liver hepatocellular carcinoma (LIHC) comprises most cases of liver cancer with a poor prognosis. N6 -methyladenosine (m6A) plays important biological functions in cancers. Thus, the present research was aimed to determine biomarkers of m6A regulators that could effectively predict the prognosis of LIHC patients. Based on the data collected from the Cancer Genome Atlas (TCGA) database, the correlation
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Construction and characterization of rectal cancer-related lncRNA-mRNA ceRNA network reveals prognostic biomarkers in rectal cancer. IET Syst. Biol. (IF 2.3) Pub Date : 2021-10-06 Guoying Cai,Meifei Sun,Xinrong Li,Junquan Zhu
Rectal cancer is an important cause of cancer-related deaths worldwide. In this study, the differentially expressed (DE) lncRNAs/mRNAs were first identified and the correlation level between DE lncRNAs and mRNAs were calculated. The results showed that genes of highly correlated lncRNA-mRNA pairs presented strong prognosis effects, such as GPM6A, METTL24, SCN7A, HAND2-AS1 and PDZRN4. Then, the rectal
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Multi-model fusion of classifiers for blood pressure estimation. IET Syst. Biol. (IF 2.3) Pub Date : 2021-09-01 Qi Ye,Bingo Wing-Kuen Ling,Nuo Xu,Yuxin Lin,Lingyue Hu
Prehypertension is a new risky disease defined in the seventh report issued by the Joint National Commission. Hence, detecting prehypertension in time plays a very important role in protecting human lives. This study proposes a method for categorising blood pressure values into two classes, namely the class of healthy blood pressure values and the class of prehypertension blood pressure values, as
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Comprehensive investigation of RNA-sequencing dataset reveals the hub genes and molecular mechanisms of coronavirus disease 2019 acute respiratory distress syndrome. IET Syst. Biol. (IF 2.3) Pub Date : 2021-08-05 Wangsheng Deng,Jiaxing Zeng,Shunyu Lu,Chaoqian Li
The goal of this study is to reveal the hub genes and molecular mechanisms of the coronavirus disease 2019 (COVID-19) acute respiratory distress syndrome (ARDS) based on the genome-wide RNA sequencing dataset. The RNA sequencing dataset of COVID-19 ARDS was obtained from GSE163426. A total of 270 differentially expressed genes (DEGs) were identified between COVID-19 ARDS and control group patients
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Variable structure robust controller design for blood glucose regulation for type 1 diabetic patients: A backstepping approach. IET Syst. Biol. (IF 2.3) Pub Date : 2021-07-08 Mohamadreza Homayounzade
Diabetes mellitus type 1 occurs when β - cells in the pancreas are destroyed by the immune system. As a result, the pancreas cannot produce adequate insulin, and the glucose enters the cells to produce energy. To elevate the glycaemic concentration, sufficient amount of insulin should be taken orally or injected into the human body. Artificial pancreas is a device that automatically regulates the level
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A two-stage neural network prediction of chronic kidney disease. IET Syst. Biol. (IF 2.3) Pub Date : 2021-06-29 Hongquan Peng,Haibin Zhu,Chi Wa Ao Ieong,Tao Tao,Tsung Yang Tsai,Zhi Liu
Accurate detection of chronic kidney disease (CKD) plays a pivotal role in early diagnosis and treatment. Measured glomerular filtration rate (mGFR) is considered the benchmark indicator in measuring the kidney function. However, due to the high resource cost of measuring mGFR, it is usually approximated by the estimated glomerular filtration rate, underscoring an urgent need for more precise and stable
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Constraint-based models for dominating protein interaction networks. IET Syst. Biol. (IF 2.3) Pub Date : 2021-05-28 Adel A Alofairi,Emad Mabrouk,Ibrahim E Elsemman
The minimum dominating set (MDSet) comprises the smallest number of graph nodes, where other graph nodes are connected with at least one MDSet node. The MDSet has been successfully applied to extract proteins that control protein-protein interaction (PPI) networks and to reveal the correlation between structural analysis and biological functions. Although the PPI network contains many MDSets, the identification
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Long non-coding RNAs and their targets as potential biomarkers in breast cancer. IET Syst. Biol. (IF 2.3) Pub Date : 2021-05-15 Maryam Khalid,Rehan Zafar Paracha,Maryum Nisar,Sumaira Malik,Salma Tariq,Iqra Arshad,Amnah Siddiqa,Zamir Hussain,Jamil Ahmad,Amjad Ali
Breast cancer is among the lethal types of cancer with a high mortality rate, globally. Its high prevalence can be controlled through improved analysis and identification of disease-specific biomarkers. Recently, long non-coding RNAs (lncRNAs) have been reported as key contributors of carcinogenesis and regulate various cellular pathways through post-transcriptional regulatory mechanisms. The specific
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Weighted gene co expression network analysis (WGCNA) with key pathways and hub-genes related to micro RNAs in ischemic stroke. IET Syst. Biol. (IF 2.3) Pub Date : 2021-05-01 Xiang Qu,Shuang Wu,Jinggui Gao,Zhenxiu Qin,Zhenhua Zhou,Jingli Liu
Ischemic stroke (IS) is one of the major causes of death and disability worldwide. However, the specific mechanism of gene interplay and the biological function in IS are not clear. Therefore, more research into IS is necessary. Dataset GSE110993 including 20 ischemic stroke (IS) and 20 control specimens are used to establish both groups and the raw RNA-seq data were analysed. Weighted gene co-expression
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Weighted gene co expression network analysis (WGCNA) with key pathways and hub-genes related to micro RNAs in ischemic stroke. IET Syst. Biol. (IF 2.3) Pub Date : 2021-05-01 Xiang Qu,Shuang Wu,Jinggui Gao,Zhenxiu Qin,Zhenhua Zhou,Jingli Liu
Ischemic stroke (IS) is one of the major causes of death and disability worldwide. However, the specific mechanism of gene interplay and the biological function in IS are not clear. Therefore, more research into IS is necessary. Dataset GSE110993 including 20 ischemic stroke (IS) and 20 control specimens are used to establish both groups and the raw RNA-seq data were analysed. Weighted gene co-expression
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Pathway-based protein-protein association network to explore mechanism of α-glucosidase inhibitors from Scutellaria baicalensis Georgi against type 2 diabetes. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-26 Le Wang,Wenbo Diwu,Nana Tan,Huan Wang,Jingbo Hu,Bailu Xu,Xiaoling Wang
Natural products have been widely used in the treatment of type 2 diabetes (T2D). However, their mechanisms are often obscured due to multi-components and multi-targets. The authors constructed a pathway-based protein-protein association (PPA) network for target proteins of 13 α-glucosidase inhibitors (AGIs) identified from Scutellaria baicalensis Georgi (SBG), designed to explore the underlying mechanisms
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Pathway-based protein-protein association network to explore mechanism of α-glucosidase inhibitors from Scutellaria baicalensis Georgi against type 2 diabetes. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-26 Le Wang,Wenbo Diwu,Nana Tan,Huan Wang,Jingbo Hu,Bailu Xu,Xiaoling Wang
Natural products have been widely used in the treatment of type 2 diabetes (T2D). However, their mechanisms are often obscured due to multi-components and multi-targets. The authors constructed a pathway-based protein-protein association (PPA) network for target proteins of 13 α-glucosidase inhibitors (AGIs) identified from Scutellaria baicalensis Georgi (SBG), designed to explore the underlying mechanisms
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Effects of noise and time delay on E2F's expression level in a bistable Rb-E2F gene's regulatory network. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-21 John Billy Kirunda,Lijian Yang,Lulu Lu,Ya Jia
The bistable Rb-E2F gene regulatory network plays a central role in regulating cellular proliferation-quiescence transition. Based on Gillespie's chemical Langevin method, the stochastic bistable Rb-E2F gene's regulatory network with time delays is proposed. It is found that under the moderate intensity of internal noise, delay in the Cyclin E synthesis rate can greatly increase the average concentration
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Effects of noise and time delay on E2F's expression level in a bistable Rb-E2F gene's regulatory network. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-21 John Billy Kirunda,Lijian Yang,Lulu Lu,Ya Jia
The bistable Rb-E2F gene regulatory network plays a central role in regulating cellular proliferation-quiescence transition. Based on Gillespie's chemical Langevin method, the stochastic bistable Rb-E2F gene's regulatory network with time delays is proposed. It is found that under the moderate intensity of internal noise, delay in the Cyclin E synthesis rate can greatly increase the average concentration
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Bifurcation analyses and potential landscapes of a cortex-basal ganglia-thalamus model. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-16 Chenri Yan,Quansheng Liu,Yuanhong Bi
The dynamics of cortical neuronal activity plays important roles in controlling body movement and is regulated by connection weights between neurons in a cortex-basal ganglia-thalamus (BGCT) loop. Beta-band oscillation of cortical activity is closely associated with the movement disorder of Parkinson's disease, which is caused by an imbalance in the connection weights of direct and indirect pathways
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Bifurcation analyses and potential landscapes of a cortex-basal ganglia-thalamus model. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-16 Chenri Yan,Quansheng Liu,Yuanhong Bi
The dynamics of cortical neuronal activity plays important roles in controlling body movement and is regulated by connection weights between neurons in a cortex-basal ganglia-thalamus (BGCT) loop. Beta-band oscillation of cortical activity is closely associated with the movement disorder of Parkinson's disease, which is caused by an imbalance in the connection weights of direct and indirect pathways
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Sliding-mode-based controllers for automation of blood glucose concentration for type 1 diabetes. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-01 Sheraz Ahmad Babar,Iftikhar Ahmad,Iqra Shafeeq Mughal
Destruction of β-cells in pancreas causes deficiency in insulin production that leads to diabetes in the human body. To cope with this problem, insulin is either taken orally during the day or injected into the patient's body using artificial pancreas (AP) during sleeping hours. Some mathematical models indicate that AP uses control algorithms to regulate blood glucose concentration (BGC). The extended
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Sliding-mode-based controllers for automation of blood glucose concentration for type 1 diabetes. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-01 Sheraz Ahmad Babar,Iftikhar Ahmad,Iqra Shafeeq Mughal
Destruction of β-cells in pancreas causes deficiency in insulin production that leads to diabetes in the human body. To cope with this problem, insulin is either taken orally during the day or injected into the patient's body using artificial pancreas (AP) during sleeping hours. Some mathematical models indicate that AP uses control algorithms to regulate blood glucose concentration (BGC). The extended
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Fuzzy logic and Lyapunov-based non-linear controllers for HCV infection. IET Syst. Biol. (IF 2.3) Pub Date : 2021-04-01 Ali Hamza,Iftikhar Ahmad,Muhammad Uneeb
Hepatitis C is the liver disease caused by the Hepatitis C virus (HCV) which can lead to serious health problems such as liver cancer. In this research work, the non-linear model of HCV having three state variables (uninfected hepatocytes, infected hepatocytes and virions) and two control inputs has been taken into account, and four non-linear controllers namely non-linear PID controller, Lyapunov