IET Systems Biology最新文献

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The mechanism of arsenic trioxide and microwave ablation in the treatment of oral squamous cell carcinoma based on high throughput sequencing 基于高通量测序的三氧化二砷和微波消融治疗口腔鳞状细胞癌的机制。
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-12-23 DOI: 10.1049/syb2.12113
Xuesong Zhang, Yakun Liu, Shengteng He, Liangjia Bi, Bing Liu
{"title":"The mechanism of arsenic trioxide and microwave ablation in the treatment of oral squamous cell carcinoma based on high throughput sequencing","authors":"Xuesong Zhang,&nbsp;Yakun Liu,&nbsp;Shengteng He,&nbsp;Liangjia Bi,&nbsp;Bing Liu","doi":"10.1049/syb2.12113","DOIUrl":"10.1049/syb2.12113","url":null,"abstract":"<p>Oral squamous cell carcinoma (OSCC) is a common head and neck malignant tumour with high incidence and poor prognosis. Arsenic trioxide (ATO) has therapeutic effects on solid tumours. Microwave ablation (MWA) has unique advantages in the treatment of solid tumours. However, the therapeutic mechanism of ATO and MWA, as well as their combined effect on OSCC were largely unelucidated. Cal-27 cell-bearing nude mice were treated with ATO and/or MWA, respectively. RNA sequencing was used to obtain gene expression profiles in tumour tissues of mice treated by ATO or MWA. RNA sequencing results were verified by real-time polymerase chain reaction (PCR). The lncRNA-miRNA-mRNA co-expression network was constructed based on the competitive endogenous RNA (ceRNA) theory. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed using differentially expressed genes. The combined effect of ATO and MWA on OSCC was evaluated. Finally, CCK-8 assay, EdU assay and transwell migration assay were performed to detect the effect of HSPA6 on the proliferation and migration of OSCC cells. The reduced volume of tumour tissues was observed in both ATO- and MWA-treated groups. 37.8% decreased in the ATO group and 35.0% in the MWA group. A total of 207 and 539 differentially expressed mRNAs and lncRNAs were identified in the ATO group. And a total of 200 and 522 differentially expressed mRNAs and lncRNAs in the MWA group were identified. The expression levels of 8 genes were verified by real-time PCR. The differentially expressed genes were closely related to “chemical carcinogenesis”, “herpes simplex infection”, “porphyrin and chlorophyll metabolism”, and “MAPK signalling pathway”. The lncRNA-miRNA-mRNA co-expression networks were constructed. The combined treatment with ATO and MWA showed a better inhibitive effect on OSCC than either of them. The synergistic effect of ATO and MWA was related to the upregulation of HSPA6. The downregulation of HSPA6 could promote the proliferation and migration of OSCC cells. This study detected the long non-coding RNA and mRNA expression profiles related to the treatment of OSCC and constructed corresponding ceRNA networks. Arsenic trioxide and MWA have a synergistic effect on OSCC, which was related to the upregulation of HSPA6.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"19 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883574","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: 0
Transcriptomic analysis reveals pathways underlying the multi-antibiotic resistance of Klebsiella pneumoniae 转录组学分析揭示了肺炎克雷伯菌多重抗生素耐药性的潜在途径。
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-12-17 DOI: 10.1049/syb2.12112
Ying Liu, Zhihui Niu, Rile Wu, Dezhi Yang, Jun Chen, Guoqing Liu, Jun Zhao
{"title":"Transcriptomic analysis reveals pathways underlying the multi-antibiotic resistance of Klebsiella pneumoniae","authors":"Ying Liu,&nbsp;Zhihui Niu,&nbsp;Rile Wu,&nbsp;Dezhi Yang,&nbsp;Jun Chen,&nbsp;Guoqing Liu,&nbsp;Jun Zhao","doi":"10.1049/syb2.12112","DOIUrl":"10.1049/syb2.12112","url":null,"abstract":"<p><i>Klebsiella pneumoniae,</i> an opportunistic pathogen, is pervasively distributed across the world. Its escalating antibiotic resistance poses a serious threat to global public health. The mechanisms behind this resistance remain largely elusive. In this study, we performed antibiotic susceptibility testing on several clinical isolates of <i>Klebsiella pneumoniae</i>, and a reference strain ATCC13883, and then analysed their transcriptomic profiles to identify genes and pathways associated with antibiotic resistance. Our results showed that a clinical isolate DY16KPN may counteract antibiotics by enhancing the biosynthesis of building blocks of bacterial cell, such as fatty acids, proteins, and DNA, and reducing transmembrane transport. Increased butanoate metabolism and lipopolysaccharide biosynthesis may also contribute to the drug-resistance of <i>Klebsiella pneumoniae</i>. Additionally, we identified resistance-promoting mutations in gene promoter regions, which regulate the activity of downstream drug-resistant genes and pathways. Our results also demonstrated that DY16KPN counterbalances the trimethoprim/sulfamethoxazole-mediated inhibitory effect on the synthesis of tetrahydrofolates and DNA by up-regulating the expression of targeted enzymes of trimethoprim/sulfamethoxazole, dihydrofolate reductase and dihydropteroate synthase.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"19 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142839668","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: 0
Analysis of type 2 diabetes mellitus-related genes by constructing the pathway-based weighted network 构建基于通路的加权网络分析2型糖尿病相关基因。
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-12-11 DOI: 10.1049/syb2.12110
Xue-Yan Zhang, Chuan-Yun Xu, Ke-Fei Cao, Hong Luo, Xu-Sheng Zhang
{"title":"Analysis of type 2 diabetes mellitus-related genes by constructing the pathway-based weighted network","authors":"Xue-Yan Zhang,&nbsp;Chuan-Yun Xu,&nbsp;Ke-Fei Cao,&nbsp;Hong Luo,&nbsp;Xu-Sheng Zhang","doi":"10.1049/syb2.12110","DOIUrl":"10.1049/syb2.12110","url":null,"abstract":"<p>Complex network is an effective approach to studying complex diseases, and provides another perspective for understanding their pathological mechanisms by illustrating the interactions between various factors of diseases. Type 2 diabetes mellitus (T2DM) is a complex polygenic metabolic disease involving genetic and environmental factors. By combining the complex network approach with biological data, this study constructs a pathway-based weighted network model of T2DM-related genes to explore the interrelationships between genes, here a weight is assigned to each edge in terms of the number of the same pathways in which the two nodes (genes) connected to the edge are involved. The edge weights can reflect differences in the strength of connections (interactions) between nodes (genes), which intuitively reflect the extent of biological correlations between genes and contribute to the importance of the nodes. Analysis of statistical and topological characteristics shows that the edge weights are correlated to the network topology, and the edge weight distribution decays as a power-law. The disparity of the weights indicates that the edge weight distribution for the nodes with the same degree is of approximately equal weights; and most edges with the higher weights tend to connect with the higher degree nodes. To determine the key hub genes of the weighted network, an integrated ranking index is used to comprehensively reflect the contribution of the three indices (strength, degree and number of pathways) of nodes; by taking the threshold of integrated ranking index greater than 0.56, 12 key hub genes are identified: <i>MAPK1</i>, <i>PIK3CD</i>, <i>PIK3CA</i>, <i>PIK3R1</i>, <i>AKT2</i>, <i>AKT1</i>, <i>KRAS</i>, <i>TNF</i>, <i>MAPK8</i>, <i>PRKCA</i>, <i>IL6</i> and <i>MTOR</i>. These genes should play an important role in the occurrence and development of T2DM, and can be regarded as potential therapeutic targets for further biological and medical research on their functions in T2DM. It can be expected that combining complex network approach with other data analysis techniques can provide more clues for exploring the pathogenesis and treatment of T2DM and other complex diseases in the future.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"19 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/syb2.12110","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814845","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: 0
Identification of CCR7 and CBX6 as key biomarkers in abdominal aortic aneurysm: Insights from multi-omics data and machine learning analysis 鉴定作为腹主动脉瘤关键生物标记物的 CCR7 和 CBX6:多组学数据和机器学习分析的启示
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-11-27 DOI: 10.1049/syb2.12106
Xi Yong, Xuerui Hu, Tengyao Kang, Yanpiao Deng, Sixuan Li, Shuihan Yu, Yani Hou, Jin You, Xiaohe Dai, Jialin Zhang, Junjia Zhang, Junlin Zhou, Siyu Zhang, Jianghua Zheng, Qin Yang, Jingdong Li
{"title":"Identification of CCR7 and CBX6 as key biomarkers in abdominal aortic aneurysm: Insights from multi-omics data and machine learning analysis","authors":"Xi Yong,&nbsp;Xuerui Hu,&nbsp;Tengyao Kang,&nbsp;Yanpiao Deng,&nbsp;Sixuan Li,&nbsp;Shuihan Yu,&nbsp;Yani Hou,&nbsp;Jin You,&nbsp;Xiaohe Dai,&nbsp;Jialin Zhang,&nbsp;Junjia Zhang,&nbsp;Junlin Zhou,&nbsp;Siyu Zhang,&nbsp;Jianghua Zheng,&nbsp;Qin Yang,&nbsp;Jingdong Li","doi":"10.1049/syb2.12106","DOIUrl":"10.1049/syb2.12106","url":null,"abstract":"<p>Abdominal aortic aneurysm (AAA) is a severe vascular condition, marked by the progressive dilation of the abdominal aorta, leading to rupture if untreated. The objective of this study was to identify key biomarkers and decipher the immune mechanisms underlying AAA utilising multi-omics data analysis and machine learning techniques. Single-cell RNA sequencing disclosed a heightened presence of macrophages and CD8-positive alpha-beta T cells in AAA, highlighting their critical role in disease pathogenesis. Analysis of cell–cell communication highlighted augmented interactions between macrophages and dendritic cells derived from monocytes. Enrichment analysis of differential expression gene indicated substantial involvement of immune and metabolic pathways in AAA pathogenesis. Machine learning techniques identified CCR7 and CBX6 as key candidate biomarkers. In AAA, CCR7 expression is upregulated, whereas CBX6 expression is downregulated, both showing significant correlations with immune cell infiltration. These findings provide valuable insights into the molecular mechanisms underlying AAA and suggest potential biomarkers for diagnosis and therapeutic intervention.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 6","pages":"250-260"},"PeriodicalIF":1.9,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741142","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: 0
Identification of co-localised transcription factors based on paired motifs analysis 基于配对图案分析鉴定共定位转录因子
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-11-26 DOI: 10.1049/syb2.12104
Li Liu, Lu Han, Kaiyuan Han, Zheng Zhang, Haojiang Zhang, Lirong Zhang
{"title":"Identification of co-localised transcription factors based on paired motifs analysis","authors":"Li Liu,&nbsp;Lu Han,&nbsp;Kaiyuan Han,&nbsp;Zheng Zhang,&nbsp;Haojiang Zhang,&nbsp;Lirong Zhang","doi":"10.1049/syb2.12104","DOIUrl":"10.1049/syb2.12104","url":null,"abstract":"<p>The interaction of transcription factors (TFs) with DNA precisely regulates gene transcription. In mammalian cells, thousands of TFs often interact with DNA <i>cis</i>-regulatory elements in a combinatorial manner rather than act alone. The identification of cooperativity between TFs can help to explore the mechanism of transcriptional regulation. However, little is known about the cooperative patterns of TFs in the genome. To identify which TFs prefer co-localisation, the authors conducted a paired motif analysis in the accessible regions of the human genome based on the Poisson background model. Especially, the authors distinguish the cooperative binding TFs and the competitive binding TFs according to the distance between TF motifs. In the K562 cell line, the authors find that TFs from a same family are always competing the same binding sites, such as FOS_JUN family, whereas KLF family TFs show significant cooperative binding in the adjacency region. Furthermore, the comparative analysis across 16 human cell lines indicates that most TF combination patterns are conserved, but there are still some cell-line-specific patterns. Finally, in human prostate cancer cells (PC-3) and human prostate normal cells (RWPE-2), the authors investigate the specific TF combination patterns in the disease cell and normal cell. The results show that the cooperative binding TF pairs shared by PC-3 and RWPE-2 account for over 90%. Simultaneously, the authors also identify 26 specific TF combination pairs in PC-3 cancer cells.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 6","pages":"238-249"},"PeriodicalIF":1.9,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717601","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: 0
DDANet: A deep dilated attention network for intracerebral haemorrhage segmentation DDANet:用于脑出血分割的深度扩张注意力网络。
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-11-24 DOI: 10.1049/syb2.12103
Haiyan Liu, Yu Zeng, Hao Li, Fuxin Wang, Jianjun Chang, Huaping Guo, Jian Zhang
{"title":"DDANet: A deep dilated attention network for intracerebral haemorrhage segmentation","authors":"Haiyan Liu,&nbsp;Yu Zeng,&nbsp;Hao Li,&nbsp;Fuxin Wang,&nbsp;Jianjun Chang,&nbsp;Huaping Guo,&nbsp;Jian Zhang","doi":"10.1049/syb2.12103","DOIUrl":"10.1049/syb2.12103","url":null,"abstract":"<p>Intracranial haemorrhage (ICH) is an urgent and potentially fatal medical condition caused by brain blood vessel rupture, leading to blood accumulation in the brain tissue. Due to the pressure and damage it causes to brain tissue, ICH results in severe neurological impairment or even death. Recently, deep neural networks have been widely applied to enhance the speed and precision of ICH detection yet they are still challenged by small or subtle hemorrhages. The authors introduce DDANet, a novel haematoma segmentation model for brain CT images. Specifically, a dilated convolution pooling block is introduced in the intermediate layers of the encoder to enhance feature extraction capabilities of middle layers. Additionally, the authors incorporate a self-attention mechanism to capture global semantic information of high-level features to guide the extraction and processing of low-level features, thereby enhancing the model's understanding of the overall structure while maintaining details. DDANet also integrates residual networks, channel attention, and spatial attention mechanisms for joint optimisation, effectively mitigating the severe class imbalance problem and aiding the training process. Experiments show that DDANet outperforms current methods, achieving the Dice coefficient, Jaccard index, sensitivity, accuracy, and a specificity of 0.712, 0.601, 0.73, 0.997, and 0.998, respectively. The code is available at https://github.com/hpguo1982/DDANet.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 6","pages":"285-297"},"PeriodicalIF":1.9,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711849","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: 0
Human essential gene identification based on feature fusion and feature screening 基于特征融合和特征筛选的人类基本基因识别。
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-11-22 DOI: 10.1049/syb2.12105
Zhao-Yue Zhang, Yue-Er Fan, Cheng-Bing Huang, Meng-Ze Du
{"title":"Human essential gene identification based on feature fusion and feature screening","authors":"Zhao-Yue Zhang,&nbsp;Yue-Er Fan,&nbsp;Cheng-Bing Huang,&nbsp;Meng-Ze Du","doi":"10.1049/syb2.12105","DOIUrl":"10.1049/syb2.12105","url":null,"abstract":"<p>Essential genes are necessary to sustain the life of a species under adequate nutritional conditions. These genes have attracted significant attention for their potential as drug targets, especially in developing broad-spectrum antibacterial drugs. However, studying essential genes remains challenging due to their variability in specific environmental conditions. In this study, the authors aim to develop a powerful prediction model for identifying essential genes in humans. The authors first obtained the essential gene data from human cancer cell lines and characterised gene sequences using 7 feature encoding methods such as Kmer, the Composition of K-spaced Nucleic Acid Pairs, and Z-curve. Subsequently, feature fusion and feature optimisation strategies were employed to select the impactful features. Finally, machine learning algorithms were applied to construct the prediction models and evaluate their performance. The single-feature-based model achieved the highest area under the Receiver Operating Characteristic curve (AUC) of 0.830. After fusing and filtering these features, the classical machine learning models achieved the highest AUC at 0.823 while the deep learning model reached 0.860. Results obtained by the authors show that compared to using individual features, feature fusion and feature optimisation strategies significantly improved model performance. Moreover, the study provided an advantageous method for essential gene identification compared to other methods.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 6","pages":"227-237"},"PeriodicalIF":1.9,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693464","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: 0
Inference and analysis of cell-cell communication of non-myeloid circulating cells in late sepsis based on single-cell RNA-seq 基于单细胞 RNA-seq 对脓毒症晚期非骨髓循环细胞的细胞间通讯进行推断和分析。
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-11-22 DOI: 10.1049/syb2.12109
Yanyan Tao, Miaomiao Li, Cheng Liu
{"title":"Inference and analysis of cell-cell communication of non-myeloid circulating cells in late sepsis based on single-cell RNA-seq","authors":"Yanyan Tao,&nbsp;Miaomiao Li,&nbsp;Cheng Liu","doi":"10.1049/syb2.12109","DOIUrl":"10.1049/syb2.12109","url":null,"abstract":"<p>Sepsis is a severe systemic inflammatory syndrome triggered by infection and is a leading cause of morbidity and mortality in intensive care units (ICUs). Immune dysfunction is a hallmark of sepsis. In this study, the authors investigated cell-cell communication among lymphoid-derived leucocytes using single-cell RNA sequencing (scRNA-seq) to gain a deeper understanding of the underlying mechanisms in late-stage sepsis. The authors’ findings revealed that both the number and strength of cellular interactions were elevated in septic patients compared to healthy individuals, with several pathways showing significant alterations, particularly in conventional dendritic cells (cDCs) and plasmacytoid dendritic cells (pDCs). Notably, pathways such as CD6-ALCAM were more activated in sepsis, potentially due to T cell suppression. This study offers new insights into the mechanisms of immunosuppression and provides potential avenues for clinical intervention in sepsis.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 6","pages":"218-226"},"PeriodicalIF":1.9,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693570","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: 0
siRNAEfficacyDB: An experimentally supported small interfering RNA efficacy database siRNAEfficacyDB: 经实验支持的小干扰 RNA 药效数据库。
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-11-14 DOI: 10.1049/syb2.12102
Yang Zhang, Ting Yang, Yu Yang, Dongsheng Xu, Yucheng Hu, Shuo Zhang, Nanchao Luo, Lin Ning, Liping Ren
{"title":"siRNAEfficacyDB: An experimentally supported small interfering RNA efficacy database","authors":"Yang Zhang,&nbsp;Ting Yang,&nbsp;Yu Yang,&nbsp;Dongsheng Xu,&nbsp;Yucheng Hu,&nbsp;Shuo Zhang,&nbsp;Nanchao Luo,&nbsp;Lin Ning,&nbsp;Liping Ren","doi":"10.1049/syb2.12102","DOIUrl":"10.1049/syb2.12102","url":null,"abstract":"<p>Small interfering RNA (siRNA) has revolutionised biomedical research and drug development through precise post-transcriptional gene silencing technology. Despite its immense potential, siRNA therapy still faces technical challenges, such as delivery efficiency, targeting specificity, and molecular stability. To address these challenges and facilitate siRNA drug development, we have developed siRNAEfficacyDB, a comprehensive database that integrates experimentally validated siRNA efficacy data. This database contains 3544 siRNA records, covering 42 target genes and 5 cell lines. It provides detailed information on siRNA sequences, target genes, inhibition efficiencies, experimental techniques, cell lines, siRNA concentrations, and incubation times. siRNAEfficacyDB offers a user-friendly web interface that makes it easy to query, browse and analyse data, enabling efficient access to siRNA-related information. In summary, siRNAEfficacyDB provides a useful data foundation for siRNA drug design and optimisation, serving as a valuable resource for advancing computer-aided siRNA design research and nucleic acid drug development. siRNAEfficacyDB is freely available at https://cellknowledge.com.cn/siRNAEfficacy for non-commercial use.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 6","pages":"199-207"},"PeriodicalIF":1.9,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142631563","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: 0
Deep-GB: A novel deep learning model for globular protein prediction using CNN-BiLSTM architecture and enhanced PSSM with trisection strategy Deep-GB:利用 CNN-BiLSTM 架构和增强型 PSSM(采用三分割策略)进行球状蛋白质预测的新型深度学习模型。
IF 1.9 4区 生物学
IET Systems Biology Pub Date : 2024-11-08 DOI: 10.1049/syb2.12108
Sonia Zouari, Farman Ali, Atef Masmoudi, Sarah Abu Ghazalah, Wajdi Alghamdi, Faris A. Kateb, Nouf Ibrahim
{"title":"Deep-GB: A novel deep learning model for globular protein prediction using CNN-BiLSTM architecture and enhanced PSSM with trisection strategy","authors":"Sonia Zouari,&nbsp;Farman Ali,&nbsp;Atef Masmoudi,&nbsp;Sarah Abu Ghazalah,&nbsp;Wajdi Alghamdi,&nbsp;Faris A. Kateb,&nbsp;Nouf Ibrahim","doi":"10.1049/syb2.12108","DOIUrl":"10.1049/syb2.12108","url":null,"abstract":"<p>Globular proteins (GPs) play vital roles in a wide range of biological processes, encompassing enzymatic catalysis and immune responses. Enzymes, among these globular proteins, facilitate biochemical reactions, while others, such as haemoglobin, contribute to essential physiological functions such as oxygen transport. Given the importance of these considerations, accurately identifying Globular proteins is essential. To address the need for precise GP identification, this research introduces an innovative approach that employs a hybrid-based deep learning model called Deep-GP. We generated two datasets based on primary sequences and developed a novel feature descriptor called, Consensus Sequence-based Trisection-Position Specific Scoring Matrix (CST-PSSM). The model training phase involved the application of deep learning techniques, including the bidirectional long short-term memory network (BiLSTM), gated recurrent unit (GRU), and convolutional neural network (CNN). The BiLSTM and CNN were hybridised for ensemble learning. The CST-PSSM-based ensemble model achieved the most accurate predictive outcomes, outperforming other competitive predictors across both training and testing datasets. This demonstrates the potential of harnessing deep learning for precise GB prediction as a robust tool to expedite research, streamline drug discovery, and unveil novel therapeutic targets.</p>","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":"18 6","pages":"208-217"},"PeriodicalIF":1.9,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11665838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142607355","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: 0
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