IET Systems Biology最新文献

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A novel m6A-related prognostic signature for predicting the overall survival of hepatocellular carcinoma patients. 预测肝细胞癌患者总生存期的一种新的m6a相关预后特征。
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2022-02-01 Epub Date: 2021-10-14 DOI: 10.1049/syb2.12036
Shiyang Xie, Yaxuan Wang, Jin Huang, Guang Li
{"title":"A novel m6A-related prognostic signature for predicting the overall survival of hepatocellular carcinoma patients.","authors":"Shiyang Xie,&nbsp;Yaxuan Wang,&nbsp;Jin Huang,&nbsp;Guang Li","doi":"10.1049/syb2.12036","DOIUrl":"https://doi.org/10.1049/syb2.12036","url":null,"abstract":"<p><p>Liver hepatocellular carcinoma (LIHC) comprises most cases of liver cancer with a poor prognosis. N<sup>6</sup> -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 between the mRNA expression levels and copy number variation (CNV) patterns were determined. Higher mRNA expression resulted from the increasing number of 9 genes. Using the univariate Cox regression analysis, 11 m6A regulators that had close correlations with the LIHC prognosis were identified. In addition, under the support of the multivariate Cox regression models and the least absolute shrinkage and selection operator, a 4-gene (YTHDF2, IGF2BP3, KIAA1429, and ALKBH5) signature of m6A regulators was constructed. This signature was expected to present a prognostic value in LIHC (log-rank test p value < 0.0001). The GSE76427 (n = 94) and ICGC-LIRI-JP (n = 212) datasets were used to validate the prognostic signature, suggesting strong power to predict patients' prognosis for LIHC. To sum up, genetic alterations in m6A regulatory genes were identified as reliable and effective biomarkers for predicting the prognosis of LIHC patients.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8849219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39516666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
PPDTS: Predicting potential drug-target interactions based on network similarity. PPDTS:基于网络相似性预测潜在的药物-靶标相互作用。
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2022-02-01 Epub Date: 2021-11-16 DOI: 10.1049/syb2.12037
Wei Wang, Yongqing Wang, Yu Zhang, Dong Liu, Hongjun Zhang, Xianfang Wang
{"title":"PPDTS: Predicting potential drug-target interactions based on network similarity.","authors":"Wei Wang,&nbsp;Yongqing Wang,&nbsp;Yu Zhang,&nbsp;Dong Liu,&nbsp;Hongjun Zhang,&nbsp;Xianfang Wang","doi":"10.1049/syb2.12037","DOIUrl":"https://doi.org/10.1049/syb2.12037","url":null,"abstract":"<p><p>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 DTIs. In this work, the authors predict potential DTIs from the local structure of drug-target associations' network, which is different from the traditional global network similarity methods based on structure and ligand. A novel method called PPDTS is proposed to predict DTIs. First, according to the DTIs' network local structure, the known DTIs are converted into a binary network. Second, the Resource Allocation algorithm is used to obtain a drug-drug similarity network and a target-target similarity network. Third, a Collaborative Filtering algorithm is used with the known drug-target topology information to obtain similarity scores. Fourth, the linear combination of drug-target similarity model and the target-drug similarity model are innovatively proposed to obtain the final prediction results. Finally, the experimental performance of PPDTS has proved to be higher than that of the previously mentioned four popular network-based similarity methods, which is validated in different experimental datasets. Some of the predicted results can be supported in UniProt and DrugBank databases.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2022-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/83/cf/SYB2-16-18.PMC8849239.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39736517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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 非小细胞肺癌中RYR2突变通过下调DKK1和上调GS1-115G20.1延长生存期:加权基因共表达网络分析和风险预后模型
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2021-12-07 DOI: 10.1049/syb2.12038
Wenjun Ren, Yongwu Li, Xi Chen, Sheng Hu, Wanli Cheng, Yu Cao, Jingcheng Gao, Xia Chen, Da Xiong, Hongrong Li, Ping Wang
{"title":"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","authors":"Wenjun Ren,&nbsp;Yongwu Li,&nbsp;Xi Chen,&nbsp;Sheng Hu,&nbsp;Wanli Cheng,&nbsp;Yu Cao,&nbsp;Jingcheng Gao,&nbsp;Xia Chen,&nbsp;Da Xiong,&nbsp;Hongrong Li,&nbsp;Ping Wang","doi":"10.1049/syb2.12038","DOIUrl":"10.1049/syb2.12038","url":null,"abstract":"<p><i>RYR2</i> 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 <i>RYR2</i> mutant group (<i>n</i> = 337) and <i>RYR2</i> wild group (<i>n</i> = 634), and established Kaplan-Meier curves. The results showed that <i>RYR2</i> mutant group lived longer than the wild group (<i>p</i> = 0.027). Weighted gene co-expression network analysis (WGCNA) of differentially expressed genes (DEGs) yielded prognosis-related genes. Five mRNAs and 10 lncRNAs were selected to build survival prognostic models with other clinical features. The AUCs of 2 models are 0.622 and 0.565 for predicting survival at 3 years. Among these genes, the AUCs of <i>DKK1</i> and <i>GS1-115G20.1</i> expression levels were 0.607 and 0.560, respectively, which predicted the 3-year survival rate of NSCLC sufferers. GSEA identified an association of high <i>DKK1</i> expression with <i>TP53</i>, <i>MTOR</i>, and <i>VEGF</i> expression. Several target miRNAs interacting with <i>GS1-115G20.1</i> were observed to show the relationship with the phenotype, treatment, and survival of NSCLC. NSCLC patients with <i>RYR2</i> mutation may obtain better prognosis by down-regulating <i>DKK1</i> and up-regulating <i>GS1-115G20.1</i>.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2f/bc/SYB2-16-43.PMC8965387.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39955582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Identification of the key genes and immune infiltrating cells determined by sex differences in ischaemic stroke through co-expression network module 通过共表达网络模块鉴定缺血性脑卒中性别差异决定的关键基因和免疫浸润细胞
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2021-11-18 DOI: 10.1049/syb2.12039
Haipeng Xu, Yanzhi Ge, Yang Liu, Yang Zheng, Rong Hu, Conglin Ren, Qianqian Liu
{"title":"Identification of the key genes and immune infiltrating cells determined by sex differences in ischaemic stroke through co-expression network module","authors":"Haipeng Xu,&nbsp;Yanzhi Ge,&nbsp;Yang Liu,&nbsp;Yang Zheng,&nbsp;Rong Hu,&nbsp;Conglin Ren,&nbsp;Qianqian Liu","doi":"10.1049/syb2.12039","DOIUrl":"10.1049/syb2.12039","url":null,"abstract":"<p>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 distribution pattern of immune subtypes between male and female patients. In this study, 141 up-regulated and 61 down-regulated genes were gathered and distributed into five modules in response to their correlation degree to clinical traits. The criterion for Gene Ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway indicated that detailed analysis had the potential to enhance clinical prediction and to identify the gender-related mechanism. After that, the expression levels of hub genes were measured via the quantitative real-time PCR (qRT-PCR) method. Finally, CCL20, ICAM1 and PTGS2 were identified and these may be some promising targets for sex differences in IS. Besides, the hub genes were further verified by rat experiments. Furthermore, these CIBERSORT results showed that T cells CD8 and Monocytes may be the target for the treatment of male and female patients, respectively.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8849259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39744883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Construction and characterization of rectal cancer-related lncRNA-mRNA ceRNA network reveals prognostic biomarkers in rectal cancer 直肠癌相关lncRNA-mRNA ceRNA网络的构建和表征揭示了直肠癌预后的生物标志物
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2021-10-06 DOI: 10.1049/syb2.12035
Guoying Cai, Meifei Sun, Xinrong Li, Junquan Zhu
{"title":"Construction and characterization of rectal cancer-related lncRNA-mRNA ceRNA network reveals prognostic biomarkers in rectal cancer","authors":"Guoying Cai,&nbsp;Meifei Sun,&nbsp;Xinrong Li,&nbsp;Junquan Zhu","doi":"10.1049/syb2.12035","DOIUrl":"10.1049/syb2.12035","url":null,"abstract":"<p>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 <i>GPM6A</i>, <i>METTL24</i>, <i>SCN7A</i>, <i>HAND2-AS1</i> and <i>PDZRN4</i>. Then, the rectal cancer-related lncRNA-mRNA network was constructed based on the ceRNA theory. Topological analysis of the network revealed that the network was maintained by hub nodes and a hub subnetwork was constructed, including the hub lncRNA MIR143HG and MBNL1-SA1. Further analysis indicated that the hub subnetwork was highly related to cancer pathways, such as ‘Focal adhesion’ and ‘Wnt signalling pathway’. Hub subnetwork also had significant prognosis capability. A closed lncRNA-mRNA module was identified by bilateral network clustering. Genes in modules also showed high prognosis effects. Finally, a core lncRNA-TF crosstalk network was identified to uncover the crosstalk and regulatory mechanisms of lncRNAs and TFs by integrating ceRNA crosstalks and TF binding affinities. Some core genes, such as MEIS1, GLI3 and HAND2-AS1 were considered as the key regulators in tumourigenesis. Based on the authors’ comprehensive analysis, all these lncRNA-mRNA crosstalks provided promising clues for biological prognosis of rectal cancer.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39490334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Multi-model fusion of classifiers for blood pressure estimation 多模型融合的血压估计分类器
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2021-09-01 DOI: 10.1049/syb2.12033
Qi Ye, Bingo Wing-Kuen Ling, Nuo Xu, Yuxin Lin, Lingyue Hu
{"title":"Multi-model fusion of classifiers for blood pressure estimation","authors":"Qi Ye,&nbsp;Bingo Wing-Kuen Ling,&nbsp;Nuo Xu,&nbsp;Yuxin Lin,&nbsp;Lingyue Hu","doi":"10.1049/syb2.12033","DOIUrl":"10.1049/syb2.12033","url":null,"abstract":"<p>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 well as estimating the blood pressure values continuously only by employing photoplethysmograms. First, the denoising of photoplethysmograms is performed via a discrete cosine transform approach. Then, the features of the photoplethysmograms in both the time domain and the frequency domain are extracted. Next, the feature vectors are categorised into the two classes of blood pressure values by a multi-model fusion of the classifiers. Here, the support vector machine, the random forest and the <i>K</i>-nearest neighbour classifier are employed for performing the fusion. There are two types of blood pressure values. They are the systolic blood pressure values and the diastolic blood pressure values. For each class and each type of blood pressure values, support vector regression is used to estimate the blood pressure values. Since different classes and different types of blood pressure values are considered separately, the proposed method achieves an accurate estimation. The computed numerical simulation results show that the proposed method based on the multi-model fusion of the classifiers achieves both higher classification accuracy and higher regression accuracy than the individual classification methods.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8c/00/SYB2-15-184.PMC8675793.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39374171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Comprehensive investigation of RNA-sequencing dataset reveals the hub genes and molecular mechanisms of coronavirus disease 2019 acute respiratory distress syndrome 综合rna测序数据揭示2019冠状病毒病急性呼吸窘迫综合征枢纽基因及分子机制
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2021-08-05 DOI: 10.1049/syb2.12034
Wangsheng Deng, Jiaxing Zeng, Shunyu Lu, Chaoqian Li
{"title":"Comprehensive investigation of RNA-sequencing dataset reveals the hub genes and molecular mechanisms of coronavirus disease 2019 acute respiratory distress syndrome","authors":"Wangsheng Deng,&nbsp;Jiaxing Zeng,&nbsp;Shunyu Lu,&nbsp;Chaoqian Li","doi":"10.1049/syb2.12034","DOIUrl":"10.1049/syb2.12034","url":null,"abstract":"<p>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. Functional enrichment analysis of DEGs suggests that these DEGs may be involved in the following biological processes: response to cytokine, G-protein coupled receptor activity, ionotropic glutamate receptor signalling pathway and G-protein coupled receptor signalling pathway. By using the weighted correlation network analysis approach to analyse these DEGs, 10 hub DEGs that may play an important role in COVID-19 ARDS were identified. A total of 67 potential COVID-19 ARDS targetted drugs were identified by a complement map analysis. Immune cell infiltration analysis revealed that the levels of T cells CD4 naive, T cells follicular helper, macrophages M1 and eosinophils in COVID-19 ARDS patients were significantly different from those in control group patients. In conclusion, this study identified 10 COVID-19 ARDS-related hub DEGs and numerous potential molecular mechanisms through a comprehensive analysis of the RNA sequencing dataset and also revealed the difference in immune cell infiltration of COVID-19 ARDS.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9f/4b/SYB2-15-205.PMC8441671.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39279057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Variable structure robust controller design for blood glucose regulation for type 1 diabetic patients: A backstepping approach 1型糖尿病患者血糖调节的变结构鲁棒控制器设计:回溯方法
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2021-07-08 DOI: 10.1049/syb2.12032
Mohamadreza Homayounzade
{"title":"Variable structure robust controller design for blood glucose regulation for type 1 diabetic patients: A backstepping approach","authors":"Mohamadreza Homayounzade","doi":"10.1049/syb2.12032","DOIUrl":"10.1049/syb2.12032","url":null,"abstract":"<p>Diabetes mellitus type 1 occurs when <math>\u0000 <mrow>\u0000 <mi>β</mi>\u0000 <mo>-</mo>\u0000 </mrow></math>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 of body insulin by injecting the requisite amount of insulin into the human body. A finite-time robust feedback controller based on the Extended Bergman Minimal Model is designed here. The controller is designed utilizing the backstepping approach and is robust against the unknown external disturbance and parametric uncertainties. The stability of the system is proved using the Lyapunov theorem. The controller is exponentially stable and hence provides the finite-time convergence of the blood glucose concentration to its desired magnitude. The effectiveness of the proposed control method is shown through simulation in MATLAB/Simulink environment via comparisons with previous studies.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/38/c9/SYB2-15-173.PMC8675804.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39163460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
A two-stage neural network prediction of chronic kidney disease 慢性肾脏疾病的两阶段神经网络预测
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2021-06-29 DOI: 10.1049/syb2.12031
Hongquan Peng, Haibin Zhu, Chi Wa Ao Ieong, Tao Tao, Tsung Yang Tsai, Zhi Liu
{"title":"A two-stage neural network prediction of chronic kidney disease","authors":"Hongquan Peng,&nbsp;Haibin Zhu,&nbsp;Chi Wa Ao Ieong,&nbsp;Tao Tao,&nbsp;Tsung Yang Tsai,&nbsp;Zhi Liu","doi":"10.1049/syb2.12031","DOIUrl":"10.1049/syb2.12031","url":null,"abstract":"<p>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 approaches. With the introduction of novel machine learning methodologies, prediction performance is shown to be significantly improved across all available data, but the performance is still limited because of the lack of models in dealing with ultra-high dimensional datasets. This study aims to provide a two-stage neural network approach for prediction of GFR and to suggest some other useful biomarkers obtained from the blood metabolites in measuring GFR. It is a composite of feature shrinkage and neural network when the number of features is much larger than the number of training samples. The results show that the proposed method outperforms the existing ones, such as convolutionneural network and direct deep neural network.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/71/55/SYB2-15-163.PMC8675857.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39038177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Constraint-based models for dominating protein interaction networks 支配蛋白质相互作用网络的约束模型
IF 2.3 4区 生物学
IET Systems Biology Pub Date : 2021-05-28 DOI: 10.1049/syb2.12021
Adel A. Alofairi, Emad Mabrouk, Ibrahim E. Elsemman
{"title":"Constraint-based models for dominating protein interaction networks","authors":"Adel A. Alofairi,&nbsp;Emad Mabrouk,&nbsp;Ibrahim E. Elsemman","doi":"10.1049/syb2.12021","DOIUrl":"10.1049/syb2.12021","url":null,"abstract":"<p>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 of multiple MDSets is an NP-complete problem, and it is difficult to determine the best MDSets, enriched with biological functions. Therefore, the MDSet model needs to be further expanded and validated to find constrained solutions that differ from those generated by the traditional models. Moreover, by identifying the critical set of the network, the set of nodes common to all MDSets can be time-consuming. Herein, the authors adopted the minimisation of metabolic adjustment (MOMA) algorithm to develop a new framework, called maximisation of interaction adjustment (MOIA). In MOIA, they provide three models; the first one generates two MDSets with a minimum number of shared proteins, the second model generates constrained multiple MDSets (<math>\u0000 <mrow>\u0000 <mi>k</mi>\u0000 </mrow></math>-MDSets), and the third model generates user-defined MDSets, containing the maximum number of essential genes and/or other important genes of the PPI network. In practice, these models significantly reduce the cost of finding the critical set and classifying the graph nodes. Herein, the authors termed the critical set as the <math>\u0000 <mrow>\u0000 <mi>k</mi>\u0000 </mrow></math>-critical set, where <math>\u0000 <mrow>\u0000 <mi>k</mi>\u0000 </mrow></math> is the number of MDSets generated by the proposed model. Then, they defined a new set of proteins called the <math>\u0000 <mrow>\u0000 <mo>(</mo>\u0000 <mi>k</mi>\u0000 <mo>−</mo>\u0000 <mn>1</mn>\u0000 <mo>)</mo>\u0000 </mrow></math>-critical set, where each node belongs to <math>\u0000 <mrow>\u0000 <mo>(</mo>\u0000 <mi>k</mi>\u0000 <mo>−</mo>\u0000 <mn>1</mn>\u0000 <mo>)</mo>\u0000 </mrow></math> MDSets. This set has been shown to be as important as the <math>\u0000 <mrow>\u0000 <mi>k</mi>\u0000 </mrow></math>-critical set and contains many essential genes, transcription factors, and protein kinases as the <math>\u0000 <mrow>\u0000 <mi>k</mi>\u0000 </mrow></math>-critical set. The <math>\u0000 <mrow>\u0000 <mo>(</mo>\u0000 <mi>k</mi>\u0000 <mo>−</mo>\u0000 <mn>1</mn>\u0000 <mo>)</mo>\u0000 </mrow></math>-critical set can be used to extend the search for drug target proteins. Based on the performance of the MOIA mod","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38959855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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