Genomics, proteomics & bioinformatics最新文献_第2页

Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment.

Genomics, proteomics & bioinformatics Pub Date : 2025-02-27 DOI: 10.1093/gpbjnl/qzaf017

Zheng Jia, Yaqing Liu, Shoufang Qu, Wenbin Li, Lin Gao, Lin Dong, Yun Xing, Yadi Cheng, Huan Fang, Yuting Yi, Yuxing Chu, Chao Zhang, Yanming Xie, Chunli Wang, Zhe Li, Zhihong Zhang, Zhipeng Xu, Yang Wang, Wenxin Zhang, Xiaoping Gu, Shuang Yang, Jinghua Li, Liangshen Wei, Yuanting Zheng, Guohui Ding, Leming Shi, Xin Yi, Jianming Ying, Jie Huang

{"title":"Evaluative Methodology for HRD Testing: Development of Standard Tools for Consistency Assessment.","authors":"Zheng Jia, Yaqing Liu, Shoufang Qu, Wenbin Li, Lin Gao, Lin Dong, Yun Xing, Yadi Cheng, Huan Fang, Yuting Yi, Yuxing Chu, Chao Zhang, Yanming Xie, Chunli Wang, Zhe Li, Zhihong Zhang, Zhipeng Xu, Yang Wang, Wenxin Zhang, Xiaoping Gu, Shuang Yang, Jinghua Li, Liangshen Wei, Yuanting Zheng, Guohui Ding, Leming Shi, Xin Yi, Jianming Ying, Jie Huang","doi":"10.1093/gpbjnl/qzaf017","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf017","url":null,"abstract":"Homologous recombination deficiency (HRD) has emerged as a critical prognostic and predictive biomarker in oncology. However, current testing methods, especially those reliant on targeted panels, are plagued by inconsistent results from the same samples. This highlights the urgent need for standardized benchmarks to evaluate HRD assay performance. In phases IIa and IIb of the Chinese HRD Harmonization Project, we developed ten pairs of well-characterized DNA reference materials derived from lung, breast, and melanoma cancer cell lines and their matched normal cell lines, each paired with seven cancer-to-normal mass ratios. Reference datasets for allele-specific copy number variations (ASCNVs) and HRD scores were established and validated based on three sequencing methods and nine analytical pipelines. The Genomic Instability Scores (GIS) of the reference materials ranged from 11 to 96, enabling validation across various thresholds. The ASCNV reference datasets covered a genomic span of 2340 to 2749 Mb, equivalent to 81.2% to 95.4% of the autosomes in the 37d5 reference genome. These benchmarks were subsequently utilized to assess the accuracy and reproducibility of four HRD panel assays, revealing significant variability in both ASCNV detection and HRD scores. The concordance between panel-detected GIS and reference GIS ranged from 0.81 to 0.94, and only two assays exhibited high overall agreement with Myriad MyChoice CDx for HRD classification. This study also identified specific challenges in ASCNV detection in HRD-related regions and the profound impact of high ploidy on consistency. The established HRD reference materials and datasets provide a robust toolkit for objective evaluation of HRD testing.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MS-based Solutions for Single Cell Proteomics. 基于 MS 的单细胞蛋白质组学解决方案。

Genomics, proteomics & bioinformatics Pub Date : 2025-02-22 DOI: 10.1093/gpbjnl/qzaf012

Siqi Li, Shuwei Li, Siqi Liu, Yan Ren

引用次数: 0

The Updated Genome Warehouse: Enhancing Data Value, Security, and Usability to Address Data Expansion.

Genomics, proteomics & bioinformatics Pub Date : 2025-02-20 DOI: 10.1093/gpbjnl/qzaf010

Yingke Ma, Xuetong Zhao, Yaokai Jia, Zhenxian Han, Caixia Yu, Zhuojing Fan, Zhang Zhang, Jingfa Xiao, Wenming Zhao, Yiming Bao, Meili Chen

{"title":"The Updated Genome Warehouse: Enhancing Data Value, Security, and Usability to Address Data Expansion.","authors":"Yingke Ma, Xuetong Zhao, Yaokai Jia, Zhenxian Han, Caixia Yu, Zhuojing Fan, Zhang Zhang, Jingfa Xiao, Wenming Zhao, Yiming Bao, Meili Chen","doi":"10.1093/gpbjnl/qzaf010","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf010","url":null,"abstract":"The Genome Warehouse (GWH), accessible at https://ngdc.cncb.ac.cn/gwh, is an extensively utilized public repository dedicated to the deposition, management and sharing of genome assembly sequences, annotations, and metadata. This paper highlights noteworthy enhancements to the GWH since the 2021 version, emphasizing substantial advancements in web interfaces for data submission, database functionality updates, and resource integration. Key updates include the reannotation of released prokaryotic genomes, mirroring of genome resources from National Center for Biotechnology Information (NCBI) GenBank and Reference Sequence Database (RefSeq), integration of Poxviridae sequences, implementation of an online batch submission system, enhancements to the quality control system, advanced search capabilities, and the introduction of a controlled-access mechanism for human genome data. These improvements collectively augment the ease and security of data submission and access as well as genome data value, thereby fostering heightened convenience and utility for researchers in the genomics field.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143470397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data. Deconer：使用基因表达数据对基于参考的解卷积方法进行评估的工具包。

Genomics, proteomics & bioinformatics Pub Date : 2025-02-18 DOI: 10.1093/gpbjnl/qzaf009

Wei Zhang, Xianglin Zhang, Qiao Liu, Lei Wei, Xu Qiao, Rui Gao, Zhiping Liu, Xiaowo Wang

{"title":"Deconer: An Evaluation Toolkit for Reference-based Deconvolution Methods Using Gene Expression Data.","authors":"Wei Zhang, Xianglin Zhang, Qiao Liu, Lei Wei, Xu Qiao, Rui Gao, Zhiping Liu, Xiaowo Wang","doi":"10.1093/gpbjnl/qzaf009","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf009","url":null,"abstract":"In recent years, computational methods for quantifying cell type proportions from transcription data have gained significant attention, particularly those reference-based methods which have demonstrated high accuracy. However, there is currently a lack of comprehensive evaluation and guidance for available reference-based deconvolution methods in cell proportion deconvolution analysis. In this study, we introduce Deconvolution Evaluator (Deconer), a comprehensive toolkit for the evaluation of reference-based deconvolution methods. Deconer provides various simulated and real gene expression datasets, including both bulk and single-cell sequencing data, and offers multiple visualization interfaces. By utilizing Deconer, we conducted systematic comparisons of 16 reference-based deconvolution methods from different perspectives, including method robustness, accuracy in deconvolving rare components, signature gene selection, and building external reference. We also performed an in-depth analysis of the application scenarios and challenges in cell proportion deconvolution methods. Finally, we provided constructive suggestions for users in selecting and developing cell proportion deconvolution algorithms. This work presents novel insights to researchers, assisting them in choosing appropriate toolkits, applying solutions in clinical contexts, and advancing the development of deconvolution tools tailored to gene expression data. The tutorials, manual, source code, and demo data of Deconer are publicly available at https://honchkrow.github.io/Deconer/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

NSUN2-mediated HCV RNA m5C Methylation Facilitates Viral RNA Stability and Replication.

Genomics, proteomics & bioinformatics Pub Date : 2025-02-17 DOI: 10.1093/gpbjnl/qzaf008

Zhu-Li Li, Yan Xie, Yafen Wang, Jing Wang, Xiang Zhou, Xiao-Lian Zhang

{"title":"NSUN2-mediated HCV RNA m5C Methylation Facilitates Viral RNA Stability and Replication.","authors":"Zhu-Li Li, Yan Xie, Yafen Wang, Jing Wang, Xiang Zhou, Xiao-Lian Zhang","doi":"10.1093/gpbjnl/qzaf008","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf008","url":null,"abstract":"RNA modifications have emerged as new efficient targets against viruses. However, little is known about 5-methylcytosine (m5C) modification in the genomes of Flaviviruses. Herein, we demonstrate that hepatitis C virus (HCV), dengue virus, and Zika virus contain high levels of viral RNA m5C modification. We find that m5C modification in HCV RNA genome is located at C7525 site in the viral NS5A gene. HCV infection increases host m5C machinery NSUN2 expression via transcription factor E2F1. Deficiency of NSUN2 decreases HCV RNA m5C methylation levels, which further reduces viral RNA stability, replication as well as viral assembly and budding. HCV RNA genomic m5C specific abrogating mutation at C7525 site reduces viral replication, assembly, and budding through decreasing viral RNA stability. Deficiency of NSUN2 also reduces host global messenger RNA (mRNA) m5C modification levels during HCV infection, which upregulates antiviral innate immune response genes expression and further suppresses HCV RNA replication. Supported by both cellular and mouse infection models, our findings reveal that NSUN2-mediated HCV RNA and host mRNA m5C methylations facilitate viral RNA replication. HCV infection promotes host NSUN2 expression to facilitate HCV replication, which implies a positive feedback loop. NSUN2 could be a potential new target for Flavivirus therapeutics.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Resolving Leukemia Heterogeneity and Lineage Aberrations with HematoMap.

Genomics, proteomics & bioinformatics Pub Date : 2025-02-13 DOI: 10.1093/gpbjnl/qzaf005

Yuting Dai, Wen Ouyang, Wen Jin, Fan Zhang, Wenyan Cheng, Jianfeng Li, Shuo He, Junqi Zong, Shijia Cao, Chenxin Zhou, Junchen Luo, Gang Lu, Jinyan Huang, Hai Fang, Xiaojian Sun, Kankan Wang, Saijuan Chen

{"title":"Resolving Leukemia Heterogeneity and Lineage Aberrations with HematoMap.","authors":"Yuting Dai, Wen Ouyang, Wen Jin, Fan Zhang, Wenyan Cheng, Jianfeng Li, Shuo He, Junqi Zong, Shijia Cao, Chenxin Zhou, Junchen Luo, Gang Lu, Jinyan Huang, Hai Fang, Xiaojian Sun, Kankan Wang, Saijuan Chen","doi":"10.1093/gpbjnl/qzaf005","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf005","url":null,"abstract":"Precise mapping of leukemic cells onto the known hematopoietic hierarchy is important for understanding the cell-of-origin and mechanisms underlying disease initiation and development. However, this task remains challenging because of the high interpatient and intrapatient heterogeneity of leukemia cell clones as well as the differences existed between leukemic and normal hematopoietic cells. Using single-cell RNA sequencing (scRNA-seq) data with a curated clustering approach, we constructed a comprehensive reference hierarchy of normal hematopoiesis. This reference hierarchy was accomplished through multistep clustering and annotating over 100,000 bone marrow mononuclear cells derived from 25 healthy donors. We further employed the cosine distance algorithm to develop a likelihood score, determining the similarities of leukemic cells to their putative normal counterparts. Using our scoring strategies, we mapped the cells of acute myeloid leukemia (AML) and B cell precursor acute lymphoblastic leukemia (BCP-ALL) samples to their corresponding counterparts. The reference hierarchy also facilitated bulk RNA sequencing (RNA-seq) analysis, enabling the development of a least absolute shrinkage and selection operator (LASSO) score model to reveal subtle differences in lineage aberrancy within AML or BCP-ALL patients. To facilitate interpretation and application, we have established an R-based package (HematoMap) that offers a fast, convenient, and user-friendly tool for identifying and visualizing lineage aberrations in leukemia from scRNA-seq and bulk RNA-seq data. Our tool provides curated resources and data analytics for understanding leukemogenesis, with the potential to enhance leukemia risk stratification and personalized treatments. The HematoMap is available at https://github.com/NRCTM-bioinfo/HematoMap.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments.

Genomics, proteomics & bioinformatics Pub Date : 2025-02-11 DOI: 10.1093/gpbjnl/qzaf007

Liu Zhijin, Xiongfei Zhang, Peipei Wang, Minheng Hong, Xiaochan Yan, Xiaoqiu Qi, Qian Zhao, Zhenghao Chen, Huajian Nie, Hui Li, Ziwen Li, Liye Zhang, Jiwei Qi, Chaolei He, Nguyen Van Truong, Minh D Le, Tilo Nadler, Hiroo Imai, Christian Roos, Ming Li

{"title":"Living on the Rocks: Genomic Analysis of Limestone Langurs Provides Novel Insights into the Adaptive Evolution in Extreme Karst Environments.","authors":"Liu Zhijin, Xiongfei Zhang, Peipei Wang, Minheng Hong, Xiaochan Yan, Xiaoqiu Qi, Qian Zhao, Zhenghao Chen, Huajian Nie, Hui Li, Ziwen Li, Liye Zhang, Jiwei Qi, Chaolei He, Nguyen Van Truong, Minh D Le, Tilo Nadler, Hiroo Imai, Christian Roos, Ming Li","doi":"10.1093/gpbjnl/qzaf007","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf007","url":null,"abstract":"Understanding how organisms adapt to their environments is a central question in evolutionary biology. Limestone langurs are unique among primates, as they are exclusively found in karst limestone habitats and have evolved mechanisms to tolerate high levels of mineral ions, which are typically associated with metal toxicity affecting organs, cells, and genetic material. We generated a high-quality reference genome (Tfra_5.0) for the limestone langur (Trachypithecus francoisi), along with genome re-sequencing data for 48 langurs representing 15 Trachypithecus species. Genes coding for ion channels (e.g., Na+, K+, and Ca2+) exhibited significantly accelerated evolution in limestone langurs. Limestone langur-specific mutations in Na+ and Ca2+ channels were experimentally confirmed to modify inward ion currents in vitro. Unexpectedly, scans for positive selection also identified genes involved in DNA damage response/repair pathways, a previously unknown adaption. This finding highlights an evolutionary adaptation in limestone langurs that mitigate the increased risk of DNA damage posed by elevated metal ion concentrations. Notably, a limestone langur-specific mutation (E94D) of the melanocortin 1 receptor was associated with increased basal cyclic adenosine monophosphate (cAMP) production, contributing to the species' darker coat color, which likely serves as camouflage on limestone rocks. Our findings reveal novel adaptive evolutionary mechanisms of limestone langurs and offer broader insights into organismal adaptation to extreme environments, with potential implications for understanding human health, biological evolution, and biodiversity conservation.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis.

Genomics, proteomics & bioinformatics Pub Date : 2025-02-11 DOI: 10.1093/gpbjnl/qzaf006

Zhenyang Zhang, Zitao Chen, Jinyan Teng, Shuli Liu, Qing Lin, Jun Wu, Yahui Gao, Zhonghao Bai, Bingjie Li, George Liu, Zhe Zhang, Yuchun Pan, Zhe Zhang, Lingzhao Fang, Qishan Wang

{"title":"FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis.","authors":"Zhenyang Zhang, Zitao Chen, Jinyan Teng, Shuli Liu, Qing Lin, Jun Wu, Yahui Gao, Zhonghao Bai, Bingjie Li, George Liu, Zhe Zhang, Yuchun Pan, Zhe Zhang, Lingzhao Fang, Qishan Wang","doi":"10.1093/gpbjnl/qzaf006","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf006","url":null,"abstract":"Transcriptome-wide association study (TWAS) is a powerful approach for investigating the molecular mechanisms linking genetic loci to complex phenotypes. However, the complexity of the TWAS analytical pipeline including the construction of gene expression reference panels, gene expression prediction, and association analysis using data from genome-wide association studies (GWAS) poses challenges for genetic studies in many species. In this study, we provide the Farm Animal Genotype-Tissue Expression (FarmGTEx) TWAS-server, an interactive and user-friendly multispecies platform designed to streamline the translation of genetic findings across tissues and species. The server incorporates gene expression data from 49 human tissues (838 individuals), 34 pig tissues (5457 individuals), and 23 cattle tissues (4889 individuals), providing prediction models for 38,180 human genes, 21,037 pig genes, and 17,942 cattle genes. It supports genotype-based gene expression prediction, GWAS summary statistics imputation, customizable TWAS analysis, functional annotations, and result visualization. Additionally, we provide 479,203, 1208, and 657 tissue-gene-trait associations for 1129 humans traits, 41cattle traits, and 11 pigs traits, respectively. Utilizing the TWAS-server, we validated the association of the ABCD4 gene with pig teat numbers. Furthermore, we identified that pig backfat thickness may share genetic similarities with human diastolic blood pressure, sarcoidosis (Lofgren syndrome), and body mass index (BMI). The FarmGTEx TWAS-server offers a comprehensive and accessible platform for researchers to perform TWAS analyses across tissues and species. It is freely available at https://twas.farmgtex.org, with regular updates planned as the FarmGTEx project expands to include more species.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Long and Accurate: How HiFi Sequencing is Transforming Genomics.

Genomics, proteomics & bioinformatics Pub Date : 2025-02-07 DOI: 10.1093/gpbjnl/qzaf003

Bo Wang, Peng Jia, Shenghan Gao, Huanhuan Zhao, Gaoyang Zheng, Linfeng Xu, Kai Ye

引用次数: 0

Identification of Small Open Reading Frame Encoded Proteins from the Human Genome.

Genomics, proteomics & bioinformatics Pub Date : 2025-02-07 DOI: 10.1093/gpbjnl/qzaf004

Hitesh Kore, Satomi Okano, Keshava K Datta, Jackson Thorp, Parthiban Periasamy, Mayur Divate, Upekha Liyanage, Gunter Hartel, Shivashankar H Nagaraj, Harsha Gowda

{"title":"Identification of Small Open Reading Frame Encoded Proteins from the Human Genome.","authors":"Hitesh Kore, Satomi Okano, Keshava K Datta, Jackson Thorp, Parthiban Periasamy, Mayur Divate, Upekha Liyanage, Gunter Hartel, Shivashankar H Nagaraj, Harsha Gowda","doi":"10.1093/gpbjnl/qzaf004","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf004","url":null,"abstract":"One of the main goals of human genome project was to identify all the protein-coding genes. There are ∼ 20,500 protein-coding genes annotated in human reference databases. However, in the last few years, proteogenomics studies have predicted thousands of novel protein-coding regions including low molecular weight proteins encoded by small open reading frames (ORFs) in untranslated regions of messenger RNAs and non-coding RNAs. Most of these predictions are based on bioinformatics analysis and ribosome footprints. The validity of some of these small ORF (sORF) encoded proteins (SEPs) has been established following functional characterization. With the growing number of predicted novel proteins, a strategy to identify reliable candidates that warrant further studies is needed. We developed an integrated proteogenomics workflow to identify reliable set of novel protein-coding regions in the human genome based on their recurrent observations across multiple samples. Publicly available ribosome profiling and global proteomics datasets were used to establish protein-coding evidence. We predicted protein translation from 4008 ORFs based on recurrent ribosome occupancy signals across samples. In addition, we identified 825 SEPs based on proteomics data. Some of the novel protein-coding regions identified were in genome-wide association studies (GWAS) loci associated with various traits and disease phenotypes. Peptides from SEPs are also presented by major histocompatibility complex class I (MHC-I) complex similar to canonical proteins. Novel protein-coding regions reported in this study expand the current catalog of protein-coding genes and warrant experimental studies to elucidate cellular functions regulated by these proteins and their role in human diseases.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0