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基因组蛋白质组与生物信息学报（英文版）
基因组蛋白质组与生物信息学报（英文版）

杨焕明；于军

双月刊

1672-0229

journal@cspg.net

010-84097425

100101

北京市朝阳区北辰西路1-7号中国科学院北京基因组研究所

基因组蛋白质组与生物信息学报（英文版）/Journal Genomics、Proteomics & BioinformaticsCSCDCSTPCD北大核心SCI
查看更多>>Genomics, Proteomics & Bioinformatics (《基因组蛋白质组与生物信息学报》，简称GPB)创刊于2003年，是由中国科学院北京基因组研究所主办、科学出版社出版的国家级英文学术期刊，由杨焕明教授、于军教授担任主编，汪建教授、贺福初院士担任副主编。 本刊主要刊载基因组学、蛋白质组学、生物信息学及其相关领域的研究进展、综述、研究论文、实验技术与方法、研究快讯等高质量的稿件，突出刊物的学术性、前沿性、指导性和实用性。 本刊读者对象为基础医学、生命科学、农学、计算机科学领域的科研与教学人员、研究生等，以及数学、物理学领域对生物科学有兴趣的研究者。 GPB (ISSN 1672-0229，CN11-4926/Q)现为季刊，面向国内外发行，邮发代号80-113。2004年国内定价每期45元，全年180元。 欢迎赐稿和订阅! 联系人：张欣 《基因组蛋白质组与生物信息学报》编辑部 北京空港科技创业园B区6号 101300 Tel: 010-80485179 Fax: 010-80498676 E-mail：editor@genomics.org.cn Http：
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    OOCDB:A Comprehensive,Systematic,and Real-time Organs-on-a-chip Database

    Jian LiWeicheng LiangZaozao ChenXingyu Li...
    243-258页
    查看更多>>摘要：Organs-on-a-chip is a microfluidic microphysiological system that uses microfluidic tech-nology to analyze the structure and function of living human cells at the tissue and organ levels in vitro.Organs-on-a-chip technology,as opposed to traditional two-dimensional cell culture and animal models,can more closely simulate pathologic and toxicologic interactions between different organs or tissues and reflect the collaborative response of multiple organs to drugs.Despite the fact that many organs-on-a-chip-related data have been published,none of the current databases have all of the following functions:searching,downloading,as well as analyzing data and results from the literature on organs-on-a-chip.Therefore,we created an organs-on-a-chip database(OOCDB)as a platform to integrate information about organs-on-a-chip from various sources,including lit-erature,patents,raw data from microarray and transcriptome sequencing,several open-access datasets of organs-on-a-chip and organoids,and data generated in our laboratory.OOCDB con-tains dozens of sub-databases and analysis tools,and each sub-database contains various data associated with organs-on-a-chip,with the goal of providing researchers with a comprehensive,sys-tematic,and convenient search engine.Furthermore,it offers a variety of other functions,such as mathematical modeling,three-dimensional modeling,and citation mapping,to meet the needs of researchers and promote the development of organs-on-a-chip.The OOCDB is available at http://www.organchip.cn.
      原文链接:
    • 万方数据
    • 维普

    TSNAdb v2.0:The Updated Version of Tumor-specific Neoantigen Database

    Jingcheng WuWenfan ChenYuxuan ZhouYing Chi...
    259-266页
    查看更多>>摘要：In recent years,neoantigens have been recognized as ideal targets for tumor immunother-apy.With the development of neoantigen-based tumor immunotherapy,comprehensive neoantigen databases are urgently needed to meet the growing demand for clinical studies.We have built the tumor-specific neoantigen database(TSNAdb)previously,which has attracted much attention.In this study,we provide TSNAdb v2.0,an updated version of the TSNAdb.TSNAdb v2.0 offers several new features,including(1)adopting more stringent criteria for neoantigen identification,(2)providing predicted neoantigens derived from three types of somatic mutations,and(3)collecting experimentally validated neoantigens and dividing them according to the experimental level.TSNAdb v2.0 is freely available at https://pgx.zju.edu.cn/tsnadb/.
      原文链接:
    • 万方数据
    • 维普

    iHypoxia:An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals

    Ze-Xian LiuPanqin WangQingfeng ZhangShihua Li...
    267-277页
    查看更多>>摘要：Mammals have evolved mechanisms to sense hypoxia and induce hypoxic responses.Recently,high-throughput techniques have greatly promoted global studies of protein expression changes during hypoxia and the identification of candidate genes associated with hypoxia-adaptive evolution,which have contributed to the understanding of the complex regulatory net-works of hypoxia.In this study,we developed an integrated resource for the expression dynamics of proteins in response to hypoxia(iHypoxia),and this database contains 2589 expression events of 1944 proteins identified by low-throughput experiments(LTEs)and 422,553 quantitative expres-sion events of 33,559 proteins identified by high-throughput experiments from five mammals that exhibit a response to hypoxia.Various experimental details,such as the hypoxic experimental con-ditions,expression patterns,and sample types,were carefully collected and integrated.Further-more,8788 candidate genes from diverse species inhabiting low-oxygen environments were also integrated.In addition,we conducted an orthologous search and computationally identified 394,141 proteins that may respond to hypoxia among 48 animals.An enrichment analysis of human proteins identified from LTEs shows that these proteins are enriched in certain drug targets and cancer genes.Annotation of known posttranslational modification(PTM)sites in the proteins iden-tified by LTEs reveals that these proteins undergo extensive PTMs,particularly phosphorylation,ubiquitination,and acetylation.iHypoxia provides a convenient and user-friendly method for users to obtain hypoxia-related information of interest.We anticipate that iHypoxia,which is freely accessible at https://ihypoxia.omicsbio.info,will advance the understanding of hypoxia and serve as a valuable data resource.
      原文链接:
    • 万方数据
    • 维普

    ncFO:A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis

    Shunheng ZhouYu'e HuangJiani XingXu Zhou...
    278-282页
    查看更多>>摘要：Ferroptosis is a form of regulated cell death driven by the accumulation of lipid hydroperoxides.Regulation of ferroptosis might be beneficial to cancer treatment.Non-coding RNAs(ncRNAs)are a class of RNA transcripts that generally cannot encode proteins and have been demonstrated to play critical roles in regulating ferroptosis.Herein,we developed ncFO,the ncRNA-ferroptosis association database,to document the manually curated and predicted ncRNAs that are associated with ferroptosis.Collectively,ncFO contains 90 experimentally verified entries,including 46 microRNAs(miRNAs),21 long non-coding RNAs(lncRNAs),and 17 circular RNAs(circRNAs).In addition,ncFO also incorporates two online prediction tools based on the regulation and co-expression of ncRNA and ferroptosis genes.Using default parameters,we obtained 3260 predicted entries,including 598 miRNAs and 178 lncRNAs,by regulation,as well as 2,592,661 predicted entries,including 967 miRNAs and 9632 lncRNAs,by ncRNA-ferroptosis gene co-expression in more than 8000 samples across 20 cancer types.The detailed information of each entry includes ncRNA name,disease,species,tissue,target,regulation,publication time,and PubMed identifier.ncFO also provides survival analysis and differential expression analysis for ncRNAs.In summary,ncFO offers a user-friendly platform to search and predict ferroptosis-associated ncRNAs,which might facilitate research on ferroptosis and discover potential targets for cancer treatment.ncFO can be accessed at http://www.jianglab.cn/ncFO/.
      原文链接:
    • 万方数据
    • 维普

    RNA2Immune:A Database of Experimentally Supported Data Linking Non-coding RNA Regulation to The Immune System

    Jianjian WangShuang LiTianfeng WangSi Xu...
    283-291页
    查看更多>>摘要：Non-coding RNAs(ncRNAs),such as microRNAs(miRNAs),long non-coding RNAs(lncRNAs),and circular RNAs(circRNAs),have emerged as important regulators of the immune system and are involved in the control of immune cell biology,disease pathogenesis,as well as vac-cine responses.A repository of ncRNA-immune associations will facilitate our understanding of ncRNA-dependent mechanisms in the immune system and advance the development of therapeutics and prevention for immune disorders.Here,we describe a comprehensive database,RNA2Immune,which aims to provide a high-quality resource of experimentally supported database linking ncRNA regulatory mechanisms to immune cell function,immune disease,cancer immunology,and vaccines.The current version of RNA2Immune documents 50,433 immune-ncRNA associations in 42 host species,including(1)6690 ncRNA associations with immune functions involving 31 immune cell types;(2)38,672 ncRNA associations with 348 immune diseases;(3)4833 ncRNA associations with cancer immunology;and(4)238 ncRNA associations with vaccine responses involving 26 vaccine types targeting 22 diseases.RNA2Immune provides a user-friendly interface for browsing,search-ing,and downloading ncRNA-immune system associations.Collectively,RNA2Immune provides important information about how ncRNAs influence immune cell function,how dysregulation of these ncRNAs leads to pathological consequences(immune diseases and cancers),and how ncRNAs affect immune responses to vaccines.RNA2Immune is available at http://bio-bigdata.hrbmu.edu.cn/rna2immune/home.j sp.
      原文链接:
    • 万方数据
    • 维普

    CTRR-ncRNA:A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs

    Tong TangXingyun LiuRongrong WuLi Shen...
    292-299页
    查看更多>>摘要：Cancer therapy resistance and recurrence(CTRR)are the dominant causes of death in cancer patients.Recent studies have indicated that non-coding RNAs(ncRNAs)can not only reverse the resistance to cancer therapy but also are crucial biomarkers for the evaluation and prediction of CTRR.Herein,we developed CTRR-ncRNA,a knowledgebase of CTRR-associated ncRNAs,aim-ing to provide an accurate and comprehensive resource for research involving the association between CTRR and ncRNAs.Compared to most of the existing cancer databases,CTRR-ncRNA is focused on the clinical characterization of cancers,including cancer subtypes,as well as survival outcomes and responses to personalized therapy of cancer patients.Information pertain-ing to biomarker ncRNAs has also been documented for the development of personalized CTRR prediction.A user-friendly interface and several functional modules have been incorporated into the database.Based on the preliminary analysis of genotype-phenotype relationships,universal ncRNAs have been found to be potential biomarkers for CTRR.The CTRR-ncRNA is a translation-oriented knowledgebase and it provides a valuable resource for mechanistic investiga-tions and explainable artificial intelligence-based modeling.CTRR-ncRNA is freely available to the public at http://ctrr.bioinf.org.cn/.
      原文链接:
    • 万方数据
    • 维普

    VIS Atlas:A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns

    Ye ChenYuyan WangPing ZhouHao Huang...
    300-310页
    查看更多>>摘要：Integration of oncogenic DNA viruses into the human genome is a key step in most virus-induced carcinogenesis.Here,we constructed a virus integration site(VIS)Atlas database,an exten-sive collection of integration breakpoints for three most prevalent oncoviruses,human papillo-mavirus,hepatitis B virus,and Epstein-Barr virus based on the next-generation sequencing(NGS)data,literature,and experimental data.There are 63,179 breakpoints and 47,411 junctional sequences with full annotations deposited in the VIS Atlas database,comprising 47 virus genotypes and 17 disease types.The VIS Atlas database provides(1)a genome browser for NGS breakpoint quality check,visualization of VISs,and the local genomic context;(2)a novel platform to discover integration patterns;and(3)a statistics interface for a comprehensive investigation of genotype-specific integration features.Data collected in the VIS Atlas aid to provide insights into virus patho-genic mechanisms and the development of novel antitumor drugs.The VIS Atlas database is avail-able at https://www.vis-atlas.tech/.
      原文链接:
    • 万方数据
    • 维普

    PlantCADB:A Comprehensive Plant Chromatin Accessibility Database

    Ke DingShanwen SunYang LuoChaoyue Long...
    311-323页
    查看更多>>摘要：Chromatin accessibility landscapes are essential for detecting regulatory elements,illus-trating the corresponding regulatory networks,and,ultimately,understanding the molecular basis underlying key biological processes.With the advancement of sequencing technologies,a large vol-ume of chromatin accessibility data has been accumulated and integrated for humans and other mammals.These data have greatly advanced the study of disease pathogenesis,cancer survival prognosis,and tissue development.To advance the understanding of molecular mechanisms regu-lating plant key traits and biological processes,we developed a comprehensive plant chromatin accessibility database(PlantCADB)from 649 samples of 37 species.These samples are abiotic stress-related(such as heat,cold,drought,and salt;159 samples),development-related(232 sam-ples),and/or tissue-specific(376 samples).Overall,18,339,426 accessible chromatin regions(ACRs)were compiled.These ACRs were annotated with genomic information,associated genes,transcrip-tion factor footprint,motif,and single-nucleotide polymorphisms(SNPs).Additionally,PlantCADB provides various tools to visualize ACRs and corresponding annotations.It thus forms an inte-grated,annotated,and analyzed plant-related chromatin accessibility resource,which can aid in better understanding genetic regulatory networks underlying development,important traits,stress adaptations,and evolution.PlantCADB is freely available at https://bioinfor.nefu.edu.cn/Plant-CADB/.
      原文链接:
    • 万方数据
    • 维普

    WheatCENet:A Database for Comparative Co-expression Network Analysis of Allohexaploid Wheat and Its Progenitors

    Zhongqiu LiYiheng HuXuelian MaLingling Da...
    324-336页
    查看更多>>摘要：Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks.Here,using large-scale transcriptome data,we con-structed co-expression networks for diploid,tetraploid,and hexaploid wheat species,and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors,named WheatCENet.WheatCENet is a platform for searching and comparing specific functional co-expression networks,as well as identifying the related functions of the genes clustered therein.Func-tional annotations like pathways,gene families,protein-protein interactions,microRNAs(miRNAs),and several lines of epigenome data are integrated into this platform,and Gene Ontol-ogy(GO)annotation,gene set enrichment analysis(GSEA),motif identification,and other useful tools are also included.Using WheatCENet,we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1(WAPO1)has more co-expressed genes related to spike develop-ment in hexaploid wheat than its progenitors.We also found a novel motif of CCWWWWWWGG(CArG)specifically in the promoter region of WAPO-A1,suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat.WheatCENet is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat.WheatCENet is freely available at http://bioinformatics.cpolar.cn/WheatCENet and http://bioinformatics.cau.edu.cn/WheatCENet.
      原文链接:
    • 万方数据
    • 维普

    TIGER:A Web Portal of Tumor Immunotherapy Gene Expression Resource

    Zhihang ChenZiwei LuoDi ZhangHuiqin Li...
    337-348页
    查看更多>>摘要：Immunotherapy is a promising cancer treatment method;however,only a few patients benefit from it.The development of new immunotherapy strategies and effective biomarkers of response and resistance is urgently needed.Recently,high-throughput bulk and single-cell gene expression profiling technologies have generated valuable resources.However,these resources are not well organized and systematic analysis is difficult.Here,we present TIGER,a tumor immunotherapy gene expression resource,which contains bulk transcriptome data of 1508 tumor samples with clinical immunotherapy outcomes and 11,057 tumor/normal samples without clinical immunotherapy outcomes,as well as single-cell transcrip tome data of 2,116,945 immune cells from 655 samples.TIGER provides many useful modules for analyzing collected and user-provided data.Using the resource in TIGER,we identified a tumor-enriched subset of CD4+T cells.Patients with melanoma with a higher signature score of this subset have a significantly better response and survival under immunotherapy.We believe that TIGER will be helpful in understanding anti-tumor immunity mechanisms and discovering effective biomarkers.TIGER is freely accessible at http://tiger.canceromics.org/.
      原文链接:
    • 万方数据
    • 维普