Genomics, proteomics & bioinformatics最新文献_第10页

Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes. 利用人群匹配参考基因组增强全基因组测序数据中的变异调用。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae070

Shuming Guo, Zhuo Huang, Yanming Zhang, Yukun He, Xiangju Chen, Wenjuan Wang, Lansheng Li, Yu Kang, Zhancheng Gao, Jun Yu, Zhenglin Du, Yanan Chu

{"title":"Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes.","authors":"Shuming Guo, Zhuo Huang, Yanming Zhang, Yukun He, Xiangju Chen, Wenjuan Wang, Lansheng Li, Yu Kang, Zhancheng Gao, Jun Yu, Zhenglin Du, Yanan Chu","doi":"10.1093/gpbjnl/qzae070","DOIUrl":"10.1093/gpbjnl/qzae070","url":null,"abstract":"Whole-exome sequencing (WES) data are frequently used for cancer diagnosis and genome-wide association studies (GWAS), based on high-coverage read mapping, informative variant calling, and high-quality reference genomes. The center position of the currently used genome assembly, GRCh38, is now challenged by two newly published telomere-to-telomere (T2T) genomes, T2T-CHM13 and T2T-YAO, and it becomes urgent to have a comparative study to test population specificity using the three reference genomes based on real case WES data. Here, we report our analysis along this line for 19 tumor samples collected from Chinese patients. The primary comparison of the exon regions among the three references reveals that the sequences in up to ∼ 1% of target regions in T2T-YAO are widely diversified from GRCh38 and may lead to off-target in sequence capture. However, T2T-YAO still outperforms GRCh38 by obtaining 7.41% of more mapped reads. Due to more reliable read-mapping and closer phylogenetic relationship with the samples than GRCh38, T2T-YAO reduces half of variant calls of clinical significance which are mostly benign, while maintaining sensitivity in identifying pathogenic variants. T2T-YAO also outperforms T2T-CHM13 in reducing calls of Chinese-specific variants. Our findings highlight the critical need for employing population-specific reference genomes in genomic analysis to ensure accurate variant analysis and the significant benefits of tailoring these approaches to the unique genetic background of each ethnic group.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11687947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells. RAG-seq：NSR引物和转座酶标记介导的单细胞链特异性总RNA测序。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae072

Ping Xu, Zhiheng Yuan, Xiaohua Lu, Peng Zhou, Ding Qiu, Zhenghao Qiao, Zhongcheng Zhou, Li Guan, Yongkang Jia, Xuan He, Ling Sun, Youzhong Wan, Ming Wang, Yang Yu

{"title":"RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells.","authors":"Ping Xu, Zhiheng Yuan, Xiaohua Lu, Peng Zhou, Ding Qiu, Zhenghao Qiao, Zhongcheng Zhou, Li Guan, Yongkang Jia, Xuan He, Ling Sun, Youzhong Wan, Ming Wang, Yang Yu","doi":"10.1093/gpbjnl/qzae072","DOIUrl":"10.1093/gpbjnl/qzae072","url":null,"abstract":"Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cellular diversity with unprecedented resolution. However, many current methods are limited in capturing full-length transcripts and discerning strand orientation. Here, we present RAG-seq, an innovative strand-specific total RNA sequencing technique that combines not-so-random (NSR) primers with Tn5 transposase-mediated tagmentation. RAG-seq overcomes previous limitations by delivering comprehensive transcript coverage and maintaining strand orientation, which are essential for accurate quantification of overlapping genes and detection of antisense transcripts. Through optimized reverse transcription with oligo-dT primers, rRNA depletion via Depletion of Abundant Sequences by Hybridization (DASH), and linear amplification, RAG-seq enhances sensitivity and reproducibility, especially for low-input samples and single cells. Application to mouse oocytes and early embryos highlights RAG-seq's superior performance in identifying stage-specific antisense transcripts, shedding light on their regulatory roles during early development. This advancement represents a significant leap in transcriptome analysis within complex biological contexts.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11658833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolution of Plant Genome Size and Composition. 植物基因组大小和组成的进化。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae078

Bing He, Wanfei Liu, Jianyang Li, Siwei Xiong, Jing Jia, Qiang Lin, Hailin Liu, Peng Cui

引用次数: 0

RNA 5-Methylcytosine Modification: Regulatory Molecules, Biological Functions, and Human Diseases. RNA 5-甲基胞嘧啶修饰：调节分子、生物功能和人类疾病。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae063

Yanfang Lu, Liu Yang, Qi Feng, Yong Liu, Xiaohui Sun, Dongwei Liu, Long Qiao, Zhangsuo Liu

{"title":"RNA 5-Methylcytosine Modification: Regulatory Molecules, Biological Functions, and Human Diseases.","authors":"Yanfang Lu, Liu Yang, Qi Feng, Yong Liu, Xiaohui Sun, Dongwei Liu, Long Qiao, Zhangsuo Liu","doi":"10.1093/gpbjnl/qzae063","DOIUrl":"10.1093/gpbjnl/qzae063","url":null,"abstract":"RNA methylation modifications influence gene expression, and disruptions of these processes are often associated with various human diseases. The common RNA methylation modification 5-methylcytosine (m5C), which is dynamically regulated by writers, erasers, and readers, widely occurs in transfer RNAs (tRNAs), messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), enhancer RNAs (eRNAs), and other non-coding RNAs (ncRNAs). RNA m5C modification regulates metabolism, stability, nuclear export, and translation of RNA molecules. An increasing number of studies have revealed the critical roles of the m5C RNA modification and its regulators in the development, diagnosis, prognosis, and treatment of various human diseases. In this review, we summarized the recent studies on RNA m5C modification and discussed the advances in its detection methodologies, distribution, and regulators. Furthermore, we addressed the significance of RNAs modified with m5C marks in essential biological processes as well as in the development of various human disorders, from neurological diseases to cancers. This review provides a new perspective on the diagnosis, treatment, and monitoring of human diseases by elucidating the complex regulatory network of the epigenetic m5C modification.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11634542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142335110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility. N6-甲基腺苷修饰在配子发生和胚胎发生中的作用：对生育能力的影响

Genomics, proteomics & bioinformatics Pub Date : 2024-10-15 DOI: 10.1093/gpbjnl/qzae050

Yujie Wang, Chen Yang, Hanxiao Sun, Hui Jiang, Pin Zhang, Yue Huang, Zhenran Liu, Yaru Yu, Zuying Xu, Huifen Xiang, Chengqi Yi

{"title":"The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility.","authors":"Yujie Wang, Chen Yang, Hanxiao Sun, Hui Jiang, Pin Zhang, Yue Huang, Zhenran Liu, Yaru Yu, Zuying Xu, Huifen Xiang, Chengqi Yi","doi":"10.1093/gpbjnl/qzae050","DOIUrl":"10.1093/gpbjnl/qzae050","url":null,"abstract":"The most common epigenetic modification of messenger RNAs (mRNAs) is N6-methyladenosine (m6A), which is mainly located near the 3' untranslated region of mRNAs, near the stop codons, and within internal exons. The biological effect of m6A is dynamically modulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). By controlling post-transcriptional gene expression, m6A has a significant impact on numerous biological functions, including RNA transcription, translation, splicing, transport, and degradation. Hence, m6A influences various physiological and pathological processes, such as spermatogenesis, oogenesis, embryogenesis, placental function, and human reproductive system diseases. During gametogenesis and embryogenesis, genetic material undergoes significant changes, including epigenomic modifications such as m6A. From spermatogenesis and oogenesis to the formation of an oosperm and early embryogenesis, m6A changes occur at every step. m6A abnormalities can lead to gamete abnormalities, developmental delays, impaired fertilization, and maternal-to-zygotic transition blockage. Both mice and humans with abnormal m6A modifications exhibit impaired fertility. In this review, we discuss the dynamic biological effects of m6A and its regulators on gamete and embryonic development and review the possible mechanisms of infertility caused by m6A changes. We also discuss the drugs currently used to manipulate m6A and provide prospects for the prevention and treatment of infertility at the epigenetic level.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer. 整合分子生物学发现肿瘤镁含量低是结直肠癌的一个驱动因素

Genomics, proteomics & bioinformatics Pub Date : 2024-10-15 DOI: 10.1093/gpbjnl/qzae053

Rou Zhang, Meng Hu, Yu Liu, Wanmeng Li, Zhiqiang Xu, Siyu He, Ying Lu, Yanqiu Gong, Xiuxuan Wang, Shan Hai, Shuangqing Li, Shiqian Qi, Yuan Li, Yang Shu, Dan Du, Huiyuan Zhang, Heng Xu, Zongguang Zhou, Peng Lei, Hai-Ning Chen, Lunzhi Dai

{"title":"Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer.","authors":"Rou Zhang, Meng Hu, Yu Liu, Wanmeng Li, Zhiqiang Xu, Siyu He, Ying Lu, Yanqiu Gong, Xiuxuan Wang, Shan Hai, Shuangqing Li, Shiqian Qi, Yuan Li, Yang Shu, Dan Du, Huiyuan Zhang, Heng Xu, Zongguang Zhou, Peng Lei, Hai-Ning Chen, Lunzhi Dai","doi":"10.1093/gpbjnl/qzae053","DOIUrl":"10.1093/gpbjnl/qzae053","url":null,"abstract":"Magnesium (Mg) deficiency is associated with increased risk and malignancy in colorectal cancer (CRC), yet the underlying mechanisms remain elusive. Here, we used genomic, proteomic, and phosphoproteomic data to elucidate the impact of Mg deficiency on CRC. Genomic analysis identified 160 genes with higher mutation frequencies in Low-Mg tumors, including key driver genes such as KMT2C and ERBB3. Unexpectedly, initiation driver genes of CRC, such as TP53 and APC, displayed higher mutation frequencies in High-Mg tumors. Additionally, proteomic and phosphoproteomic data indicated that low Mg content in tumors may activate epithelial-mesenchymal transition (EMT) by modulating inflammation or remodeling the phosphoproteome of cancer cells. Notably, we observed a negative correlation between the phosphorylation of DBN1 at S142 (DBN1S142p) and Mg content. A mutation in S142 to D (DBN1S142D) mimicking DBN1S142p up-regulated MMP2 and enhanced cell migration, while treatment with MgCl2 reduced DBN1S142p, thereby reversing this phenotype. Mechanistically, Mg2+ attenuated the DBN1-ACTN4 interaction by decreasing DBN1S142p, which in turn enhanced the binding of ACTN4 to F-actin and promoted F-actin polymerization, ultimately reducing MMP2 expression. These findings shed new light on the crucial role of Mg deficiency in CRC progression and suggest that Mg supplementation may be a promising preventive and therapeutic strategy for CRC.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141763491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of Cancer Stem Cells in Laryngeal Squamous Cell Carcinoma by Single-cell RNA Sequencing. 通过单细胞 RNA 测序鉴定喉鳞状细胞癌中癌症干细胞的特征

Genomics, proteomics & bioinformatics Pub Date : 2024-10-15 DOI: 10.1093/gpbjnl/qzae056

Yanguo Li, Chen Lin, Yidian Chu, Zhengyu Wei, Qi Ding, Shanshan Gu, Hongxia Deng, Qi Liao, Zhisen Shen

{"title":"Characterization of Cancer Stem Cells in Laryngeal Squamous Cell Carcinoma by Single-cell RNA Sequencing.","authors":"Yanguo Li, Chen Lin, Yidian Chu, Zhengyu Wei, Qi Ding, Shanshan Gu, Hongxia Deng, Qi Liao, Zhisen Shen","doi":"10.1093/gpbjnl/qzae056","DOIUrl":"10.1093/gpbjnl/qzae056","url":null,"abstract":"Cancer stem cells (CSCs) constitute a pivotal element within the tumor microenvironment (TME), driving the initiation and progression of cancer. However, the identification of CSCs and their underlying molecular mechanisms in laryngeal squamous cell carcinoma (LSCC) remains a formidable challenge. Here, we employed single-cell RNA sequencing of matched primary tumor tissues, paracancerous tissues, and local lymph nodes from three LSCC patients to comprehensively characterize the CSCs in LSCC. Two distinct clusters of stem cells originating from epithelial populations were delineated and verified as CSCs and normal stem cells (NSCs), respectively. CSCs were abundant in the paracancerous tissues compared to those in the tumor tissues. CSCs showed high expression of stem cell marker genes such as PROM1, ALDH1A1, and SOX4, and increased the activity of tumor-related hypoxia, Wnt/β-catenin, and Notch signaling pathways. We then explored the intricate crosstalk between CSCs and the TME cells and identified targets within the TME that related with CSCs. We also found eight marker genes of CSCs that were correlated significantly with the prognosis of LSCC patients. Furthermore, bioinformatics analyses showed that drugs such as erlotinib, OSI-027, and ibrutinib selectively targeted the CSC-specifically expressed genes. In conclusion, our results represent the first comprehensive characterization of CSC properties in LSCC at the single-cell level.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141899231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comprehensive Characterization of the Integrin Family Across 32 Cancer Types. 32 种癌症类型中整合素家族的综合特征。

Genomics, proteomics & bioinformatics Pub Date : 2024-10-15 DOI: 10.1093/gpbjnl/qzae035

Cheng Zou, Jinwei Zhu, Jiangling Xiong, Yu Tian, Yousong Peng, Edwin Cheung, Dingxiao Zhang

{"title":"Comprehensive Characterization of the Integrin Family Across 32 Cancer Types.","authors":"Cheng Zou, Jinwei Zhu, Jiangling Xiong, Yu Tian, Yousong Peng, Edwin Cheung, Dingxiao Zhang","doi":"10.1093/gpbjnl/qzae035","DOIUrl":"10.1093/gpbjnl/qzae035","url":null,"abstract":"Integrin genes are widely involved in tumorigenesis. Yet, a comprehensive characterization of integrin family members and their interactome at the pan-cancer level is lacking. Here, we systematically analyzed integrin family in approximately 10,000 tumors across 32 cancer types. Globally, integrins represent a frequently altered and misexpressed pathway, with alteration and dysregulation overall being protumorigenic. Expression dysregulation, better than mutational landscape, of integrin family successfully identifies a subgroup of aggressive tumors with a high level of proliferation and stemness. The results reveal that several molecular mechanisms collectively regulate integrin expression in a context-dependent manner. For potential clinical usage, we constructed a weighted scoring system, integrinScore, to measure integrin signaling patterns in individual tumors. Remarkably, integrinScore was consistently correlated with predefined molecular subtypes in multiple cancers, with integrinScore-high tumors being more aggressive. Importantly, integrinScore was cancer-dependent and closely associated with proliferation, stemness, tumor microenvironment, metastasis, and immune signatures. IntegrinScore also predicted patients' response to immunotherapy. By mining drug databases, we unraveled an array of compounds that may modulate integrin signaling. Finally, we built a user-friendly database, Pan-cancer Integrin Explorer (PIExplorer; http://computationalbiology.cn/PIExplorer), to facilitate researchers to explore integrin-related knowledge. Collectively, we provide a comprehensive characterization of integrins across cancers and offer gene-specific and cancer-specific rationales for developing integrin-targeted therapy.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11849494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-cell RNA-seq Reveals the Inhibitory Effect of Methamphetamine on Liver Immunity with the Involvement of Dopamine Receptor D1. 单细胞 RNA 截图揭示甲基苯丙胺抑制肝脏免疫与多巴胺受体 D1 的关系

Genomics, proteomics & bioinformatics Pub Date : 2024-10-15 DOI: 10.1093/gpbjnl/qzae060

Jin-Ting Zhou, Yungang Xu, Xiao-Huan Liu, Cheng Cheng, Jing-Na Fan, Xiaoming Li, Jun Yu, Shengbin Li

{"title":"Single-cell RNA-seq Reveals the Inhibitory Effect of Methamphetamine on Liver Immunity with the Involvement of Dopamine Receptor D1.","authors":"Jin-Ting Zhou, Yungang Xu, Xiao-Huan Liu, Cheng Cheng, Jing-Na Fan, Xiaoming Li, Jun Yu, Shengbin Li","doi":"10.1093/gpbjnl/qzae060","DOIUrl":"10.1093/gpbjnl/qzae060","url":null,"abstract":"Methamphetamine (METH) is a highly addictive psychostimulant that causes physical and psychological damage and immune system disorder, especially in the liver which contains a significant number of immune cells. Dopamine, a key neurotransmitter in METH addiction and immune regulation, plays a crucial role in this process. Here, we developed a chronic METH administration model and conducted single-cell RNA sequencing (scRNA-seq) to investigate the effect of METH on liver immune cells and the involvement of dopamine receptor D1 (DRD1). Our findings reveal that chronic exposure to METH induces immune cell identity shifts from IFITM3+ macrophage (Mac) and CCL5+ Mac to CD14+ Mac, as well as from FYN+CD4+ T effector (Teff), CD8+ T, and natural killer T (NKT) to FOS+CD4+ T and RORα+ group 2 innate lymphoid cell (ILC2), along with the suppression of multiple functional immune pathways. DRD1 is implicated in regulating certain pathways and identity shifts among the hepatic immune cells. Our results provide valuable insights into the development of targeted therapies to mitigate METH-induced immune impairment.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11576359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142086421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TCRosetta: An Integrated Analysis and Annotation Platform for T-cell Receptor Sequences. TCRosetta：T 细胞受体序列的综合分析和注释平台。

Genomics, proteomics & bioinformatics Pub Date : 2024-10-15 DOI: 10.1093/gpbjnl/qzae013

Tao Yue, Si-Yi Chen, Wen-Kang Shen, Zhan-Ye Zhang, Liming Cheng, An-Yuan Guo

{"title":"TCRosetta: An Integrated Analysis and Annotation Platform for T-cell Receptor Sequences.","authors":"Tao Yue, Si-Yi Chen, Wen-Kang Shen, Zhan-Ye Zhang, Liming Cheng, An-Yuan Guo","doi":"10.1093/gpbjnl/qzae013","DOIUrl":"10.1093/gpbjnl/qzae013","url":null,"abstract":"T cells and T-cell receptors (TCRs) are essential components of the adaptive immune system. Characterization of the TCR repertoire offers a promising and highly informative source for understanding the functions of T cells in the immune response and immunotherapy. Although TCR repertoire studies have attracted much attention, there are few online servers available for TCR repertoire analysis, especially for TCR sequence annotation or advanced analyses. Therefore, we developed TCRosetta, a comprehensive online server that integrates analytical methods for TCR repertoire analysis and visualization. TCRosetta combines general feature analysis, large-scale sequence clustering, network construction, peptide-TCR binding prediction, generation probability calculation, and k-mer motif analysis for TCR sequences, making TCR data analysis as simple as possible. The TCRosetta server accepts multiple input data formats and can analyze ∼ 20,000 TCR sequences in less than 3 min. TCRosetta is the most comprehensive web server available for TCR repertoire analysis and is freely available at https://guolab.wchscu.cn/TCRosetta/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11849489/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0