Genomics, Proteomics & Bioinformatics最新文献_第9页

Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL 基于TINDL的临床前到临床抗癌药物反应预测和生物标志物鉴定。

IF 11.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-06-01 DOI: 10.1016/j.gpb.2023.01.006

David Earl Hostallero , Lixuan Wei , Liewei Wang , Junmei Cairns , Amin Emad

{"title":"Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL","authors":"David Earl Hostallero , Lixuan Wei , Liewei Wang , Junmei Cairns , Amin Emad","doi":"10.1016/j.gpb.2023.01.006","DOIUrl":"10.1016/j.gpb.2023.01.006","url":null,"abstract":"<div><div>Prediction of the response of <strong>cancer</strong> patients to different treatments and identification of biomarkers of <strong>drug response</strong> are two major goals of individualized medicine. Here, we developed a <strong>deep learning</strong> framework called TINDL, completely trained on preclinical cancer cell lines (CCLs), to predict the response of cancer patients to different treatments. TINDL utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the statistical discrepancies between CCLs and patient tumors. Moreover, by making the deep learning black box interpretable, this model identifies a small set of genes whose expression levels are predictive of drug response in the trained model, enabling identification of biomarkers of drug response. Using data from two large databases of CCLs and cancer tumors, we showed that this model can distinguish between sensitive and resistant tumors for 10 (out of 14) drugs, outperforming various other machine learning models. In addition, our small interfering RNA (siRNA) knockdown experiments on 10 genes identified by this model for one of the drugs (tamoxifen) confirmed that tamoxifen sensitivity is substantially influenced by all of these genes in MCF7 cells, and seven of these genes in T47D cells. Furthermore, genes implicated for multiple drugs pointed to shared mechanism of action among drugs and suggested several important signaling pathways. In summary, this study provides a powerful deep learning framework for prediction of drug response and identification of biomarkers of drug response in cancer. The code can be accessed at <span><span>https://github.com/ddhostallero/tindl</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 3","pages":"Pages 535-550"},"PeriodicalIF":11.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10787192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10695748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes 绘制多因子介导的染色质相互作用以评估肺癌相关基因的失调。

IF 11.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-06-01 DOI: 10.1016/j.gpb.2023.01.004

Yan Zhang , Jingwen Zhang , Wei Zhang , Mohan Wang , Shuangqi Wang , Yao Xu , Lun Zhao , Xingwang Li , Guoliang Li

{"title":"Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes","authors":"Yan Zhang , Jingwen Zhang , Wei Zhang , Mohan Wang , Shuangqi Wang , Yao Xu , Lun Zhao , Xingwang Li , Guoliang Li","doi":"10.1016/j.gpb.2023.01.004","DOIUrl":"10.1016/j.gpb.2023.01.004","url":null,"abstract":"<div><div>Studies on the <strong>lung cancer</strong> genome are indispensable for developing a cure for lung cancer. Whole-genome resequencing, genome-wide association studies, and transcriptome sequencing have greatly improved our understanding of the cancer genome. However, <strong>dysregulation</strong> of long-range <strong>chromatin interactions</strong> in lung cancer remains poorly described. To better understand the three-dimensional (3D) genomic interaction features of the lung cancer genome, we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase II (RNAPII), CCCTC-binding factor (CTCF), enhancer of zeste homolog 2 (EZH2), and histone 3 lysine 27 trimethylation (H3K27me3) using long-read chromatin interaction analysis by paired-end tag sequencing (<strong>ChIA-PET</strong>). Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes, either through loops or domains, and their distributions along the genome were distinct from and complementary to those associated with RNAPII. Cancer-related genes were highly enriched with chromatin interactions, and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes, such as additional repressive interactions on <em>FOXO4</em> and promoter–promoter interactions between <em>NF1</em> and <em>RNF135</em>. Knockout of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes, suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes. These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.</div></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 3","pages":"Pages 573-588"},"PeriodicalIF":11.5,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10787015/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10615752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues deCS：人类组织中单细胞RNA测序数据的系统细胞类型注释工具。

IF 9.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI: 10.1016/j.gpb.2022.04.001

Guangsheng Pei , Fangfang Yan , Lukas M. Simon , Yulin Dai , Peilin Jia , Zhongming Zhao

{"title":"deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues","authors":"Guangsheng Pei , Fangfang Yan , Lukas M. Simon , Yulin Dai , Peilin Jia , Zhongming Zhao","doi":"10.1016/j.gpb.2022.04.001","DOIUrl":"10.1016/j.gpb.2022.04.001","url":null,"abstract":"<div><p>Single-cell RNA sequencing (<strong>scRNA-seq</strong>) is revolutionizing the study of complex and dynamic cellular mechanisms. However, cell type annotation remains a main challenge as it largely relies on <em>a priori</em> knowledge and manual curation, which is cumbersome and subjective. The increasing number of scRNA-seq datasets, as well as numerous published genetic studies, has motivated us to build a comprehensive human cell type reference atlas.Here, we present decoding Cell type Specificity (<em>deCS</em>), an automatic <strong>cell type annotation</strong> method augmented by a comprehensive collection of human cell type expression profiles and marker genes. We used <em>deCS</em> to annotate scRNA-seq data from various tissue types and systematically evaluated the annotation accuracy under different conditions, including reference panels, sequencing depth, and feature selection strategies. Our results demonstrate that expanding the references is critical for improving annotation accuracy. Compared to many existing state-of-the-art annotation tools, <em>deCS</em> significantly reduced computation time and increased accuracy. <em>deCS</em> can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation. Finally, we demonstrated the broad utility of <em>deCS</em> to identify <strong>trait–cell type associations</strong> in 51 human complex traits, providing deep insights into the cellular mechanisms underlying disease pathogenesis. All documents for <em>deCS</em>, including source code, user manual, demo data, and tutorials, are freely available at <span>https://github.com/bsml320/deCS</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 370-384"},"PeriodicalIF":9.5,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10059212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors 小麦CENet：一个用于异六倍体小麦及其祖先比较共表达网络分析的数据库。

IF 9.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI: 10.1016/j.gpb.2022.04.007

Zhongqiu Li , Yiheng Hu , Xuelian Ma , Lingling Da , Jiajie She , Yue Liu , Xin Yi , Yaxin Cao , Wenying Xu , Yuannian Jiao , Zhen Su

{"title":"WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors","authors":"Zhongqiu Li , Yiheng Hu , Xuelian Ma , Lingling Da , Jiajie She , Yue Liu , Xin Yi , Yaxin Cao , Wenying Xu , Yuannian Jiao , Zhen Su","doi":"10.1016/j.gpb.2022.04.007","DOIUrl":"10.1016/j.gpb.2022.04.007","url":null,"abstract":"<div><p>Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed <strong>co-expression networks</strong> 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. <strong>Functional annotations</strong> like pathways, gene families, protein–protein interactions, microRNAs (miRNAs), and several lines of epigenome data are integrated into this platform, and Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using WheatCENet, we found that the network of <em>WHEAT ABERRANT PANICLE ORGANIZATION 1</em> (<em>WAPO1</em>) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CCWWWWWWGG (CArG) specifically in the promoter region of <em>WAPO-A1</em>, suggesting that neofunctionalization of the <em>WAPO-A1</em> 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 <span>http://bioinformatics.cpolar.cn/WheatCENet</span><svg><path></path></svg> and <span>http://bioinformatics.cau.edu.cn/WheatCENet</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 324-336"},"PeriodicalIF":9.5,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9779875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns VIS图谱：从NGS数据中获取人类基因组中病毒整合位点的数据库，以探索整合模式。

IF 9.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI: 10.1016/j.gpb.2023.02.005

Ye Chen , Yuyan Wang , Ping Zhou , Hao Huang , Rui Li , Zhen Zeng , Zifeng Cui , Rui Tian , Zhuang Jin , Jiashuo Liu , Zhaoyue Huang , Lifang Li , Zheying Huang , Xun Tian , Meiying Yu , Zheng Hu

{"title":"VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns","authors":"Ye Chen , Yuyan Wang , Ping Zhou , Hao Huang , Rui Li , Zhen Zeng , Zifeng Cui , Rui Tian , Zhuang Jin , Jiashuo Liu , Zhaoyue Huang , Lifang Li , Zheying Huang , Xun Tian , Meiying Yu , Zheng Hu","doi":"10.1016/j.gpb.2023.02.005","DOIUrl":"10.1016/j.gpb.2023.02.005","url":null,"abstract":"<div><p>Integration of oncogenic <strong>DNA viruses</strong> into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed a <strong>virus integration site</strong> (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein–Barr virus based on the <strong>next-generation sequencing</strong> (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 <strong>virus genotypes</strong> 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 <strong>integration patterns</strong>; 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 pathogenic mechanisms and the development of novel antitumor drugs. The VIS Atlas database is available at <span>https://www.vis-atlas.tech/</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 300-310"},"PeriodicalIF":9.5,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10149144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants RegVar：非编码调控变体的组织特异性优先级。

IF 9.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI: 10.1016/j.gpb.2021.08.011

Hao Lu, Luyu Ma, Cheng Quan, Lei Li, Yiming Lu, Gangqiao Zhou, Chenggang Zhang

{"title":"RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants","authors":"Hao Lu, Luyu Ma, Cheng Quan, Lei Li, Yiming Lu, Gangqiao Zhou, Chenggang Zhang","doi":"10.1016/j.gpb.2021.08.011","DOIUrl":"10.1016/j.gpb.2021.08.011","url":null,"abstract":"<div><p>Non-coding genomic variants constitute the majority of trait-associated genome variations; however, the identification of functional non-coding variants is still a challenge in human genetics, and a method for systematically assessing the impact of regulatory variants on gene expression and linking these regulatory variants to potential target genes is still lacking. Here, we introduce a deep neural network (DNN)-based computational framework, RegVar, which can accurately predict the tissue-specific impact of non-coding regulatory variants on target genes. We show that by robustly learning the genomic characteristics of massive variant–gene expression associations in a variety of human tissues, RegVar vastly surpasses all current non-coding variant prioritization methods in predicting regulatory variants under different circumstances. The unique features of RegVar make it an excellent framework for assessing the regulatory impact of any variant on its putative target genes in a variety of tissues. RegVar is available as a web server at <span>https://regvar.omic.tech/</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 385-395"},"PeriodicalIF":9.5,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39866008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis ncFO：与Ferroptosis相关的已治愈和预测的ncRNA的综合资源。

IF 9.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI: 10.1016/j.gpb.2022.09.004

Shunheng Zhou , Yu’e Huang , Jiani Xing , Xu Zhou , Sina Chen , Jiahao Chen , Lihong Wang , Wei Jiang

{"title":"ncFO: A Comprehensive Resource of Curated and Predicted ncRNAs Associated with Ferroptosis","authors":"Shunheng Zhou , Yu’e Huang , Jiani Xing , Xu Zhou , Sina Chen , Jiahao Chen , Lihong Wang , Wei Jiang","doi":"10.1016/j.gpb.2022.09.004","DOIUrl":"10.1016/j.gpb.2022.09.004","url":null,"abstract":"<div><p><strong>Ferroptosis</strong> is a form of regulated cell death driven by the accumulation of lipid hydroperoxides. Regulation of ferroptosis might be beneficial to <strong>cancer</strong> 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 <strong>microRNAs</strong> (miRNAs), 21 <strong>long non-coding RNAs</strong> (lncRNAs), and 17 <strong>circular RNAs</strong> (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 <span>http://www.jianglab.cn/ncFO/</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 278-282"},"PeriodicalIF":9.5,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9740275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

TSNAdb v2.0: The Updated Version of Tumor-specific Neoantigen Database TSNAdb v2.0：肿瘤特异性新抗原数据库的更新版本。

IF 9.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI: 10.1016/j.gpb.2022.09.012

Jingcheng Wu , Wenfan Chen , Yuxuan Zhou , Ying Chi , Xiansheng Hua , Jian Wu , Xun Gu , Shuqing Chen , Zhan Zhou

引用次数: 5

OOCDB: A Comprehensive, Systematic, and Real-time Organs-on-a-chip Database OOCDB：一个全面、系统、实时的片上组织数据库。

IF 9.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI: 10.1016/j.gpb.2023.01.001

Jian Li , Weicheng Liang , Zaozao Chen , Xingyu Li , Pan Gu , Anna Liu , Pin Chen , Qiwei Li , Xueyin Mei , Jing Yang , Jun Liu , Lincao Jiang , Zhongze Gu

{"title":"OOCDB: A Comprehensive, Systematic, and Real-time Organs-on-a-chip Database","authors":"Jian Li , Weicheng Liang , Zaozao Chen , Xingyu Li , Pan Gu , Anna Liu , Pin Chen , Qiwei Li , Xueyin Mei , Jing Yang , Jun Liu , Lincao Jiang , Zhongze Gu","doi":"10.1016/j.gpb.2023.01.001","DOIUrl":"10.1016/j.gpb.2023.01.001","url":null,"abstract":"<div><p><strong>Organs-on-a-chip</strong> is a microfluidic microphysiological system that uses microfluidic technology to analyze the structure and function of living human cells at the tissue and <strong>organ</strong> levels <em>in vitro</em>. 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 <strong>databases</strong> 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 literature, 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 contains 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, systematic, and convenient search engine. Furthermore, it offers a variety of other functions, such as <strong>mathematical modeling</strong>, three-dimensional modeling, and <strong>citation mapping</strong>, to meet the needs of researchers and promote the development of organs-on-a-chip. The OOCDB is available at <span>http://www.organchip.cn</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 243-258"},"PeriodicalIF":9.5,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9752429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PlantCADB: A Comprehensive Plant Chromatin Accessibility Database PlantCADB:一个全面的植物染色质可访问性数据库。

IF 9.5 2区生物学

Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI: 10.1016/j.gpb.2022.10.005

Ke Ding , Shanwen Sun , Yang Luo , Chaoyue Long , Jingwen Zhai , Yixiao Zhai , Guohua Wang

{"title":"PlantCADB: A Comprehensive Plant Chromatin Accessibility Database","authors":"Ke Ding , Shanwen Sun , Yang Luo , Chaoyue Long , Jingwen Zhai , Yixiao Zhai , Guohua Wang","doi":"10.1016/j.gpb.2022.10.005","DOIUrl":"10.1016/j.gpb.2022.10.005","url":null,"abstract":"<div><p><strong>Chromatin accessibility</strong> landscapes are essential for detecting regulatory elements, illustrating the corresponding <strong>regulatory networks</strong>, and, ultimately, understanding the molecular basis underlying key biological processes. With the advancement of sequencing technologies, a large volume 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 regulating <strong>plant</strong> 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 samples), 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, <strong>transcription factor footprint</strong>, motif, and single-nucleotide polymorphisms (SNPs). Additionally, PlantCADB provides various tools to visualize ACRs and corresponding annotations. It thus forms an integrated, 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 <span>https://bioinfor.nefu.edu.cn/PlantCADB/</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 311-323"},"PeriodicalIF":9.5,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9767481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1