检索结果-南通市图书馆

A Brief Review on the Human Encyclopedia of DNA Elements (ENCODE) Project

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2013年第3期11卷 135-141页

作者： Hongzhu Qu xiangdong fang CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

The ENCyclopedia Of DNA Elements （ENCODE） project is an international research consortium that aims to identify all functional elements in the human genome sequence. The second phase of the project comprised 1640 datasets from 147 different cell types, yielding a set of 30 publications across several journals. These data revealed that 80.4% of the human genome displays some functionality in at least one cell type. Many of these regulatory elements are physically asso- ciated with one another and further form a network or three-dimensional conformation to affect gene expression. These elements are also related to sequence variants associated with diseases or traits. All these findings provide us new insights into the organization and regulation of genes and genome, and serve as an expansive resource for understanding human health and disease.

关键词： ENCODE project Chromatin structure Transcription factors DNA methylation

Big Data and the Brain: Peeking at the Future

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2019年第4期17卷 333-336页

作者： Hongzhu Qu Hongxing Lei xiangdong fang CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Sino-Danish College University of Chinese Academy of SciencesBeijing 100049China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

The era of brain science across the world The human brain is the most complex organ in the human *** comprises billions of neurons and supporting cells in a complex network,managing everything from physical functions to thoughts and feelings of *** of the complex network caused by both genetic and environmental factors result in many brain *** large brain projects have been launched,aiming to understand how the brain works in health and disease,including the Human Brain Project of the European Union,the Brain Research through Advancing Innovative Neurotechnologies(BRAIN)Initiative of the United States,and the Brain Mapping by Integrated Neurotechnologies for Disease Studies(Brain/MIND)project of Japan.

关键词： Brain supporting network

GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2019年第4期17卷 465-471页

作者： Yadong Yang Yang Sui Bingbing Xie Hongzhu Qu xiangdong fang CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Gliomas are one of the most common types of brain *** efforts have been devoted to studying the mechanisms of glioma genesis and identifying biomarkers for diagnosis and *** help further investigations,we present a comprehensive database named *** includes 21,086 samples from 4303 patients and integrates genomic,transcriptomic,epigenomic,clinical,and gene-drug association data regarding glioblastoma multiforme(GBM)and low-grade glioma(LGG)from The Cancer Genome Atlas(TCGA),Gene Expression Omnibus(GEO),the Chinese Glioma Genome Atlas(CGGA),the Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets(MSK-IMPACT),the US Food and Drug Administration(FDA),and Pharm *** offers a user-friendly interface for two main types of *** first comprises queries of(i)somatic mutations,(ii)gene expression,(iii)microRNA(miRNA)expression,and(iv)DNA *** addition,queries can be executed at the gene,region,and base ***,GliomaDB allows users to perform survival analysis,coexpression network visualization,multi-omics data visualization,and targeted drug recommendations based on personalized *** bridges the gap between glioma genomics big data and the delivery of integrated information for end users,thus enabling both researchers and clinicians to effectively use publicly available data and empowering the progression of precision medicine in *** is freely accessible at http://***/glioma DB.

关键词： Database Variations Methylation Network Survival analysis

Biomarker Profiling for Lupus Nephritis

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2013年第3期11卷 158-165页

作者： Yajuan Li xiangdong fang Quan-Zhen Li Department of Immunology and Internal Medicine The University of Texas Southwestern Medical Center CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

Lupus nephritis （LN） is one of the most severe manifestations of systemic lupus erythematosus （SLE）, which is associated with significant morbidity and mortality of SLE patients. The pathogenesis of LN involves multiple factors, including genetic predisposition, epigenetic regulation and environmental interaction. Over the last decade, omics-based techniques have been extensively utilized for biomarker screening and a wide variety of variations which are associated with SLE and LN have been identified at the levels of genomics, transcriptomics and proteomics. These studies and discoveries have expanded our understanding of the molecular basis of the disease and are important for identification of potential therapeutic targets for disease prediction and early treat- ment. In this review, we summarize some of the recent studies targeted at the identification of LN-associated biomarkers using genomics and proteomic approaches.

关键词： Lupus nephritisGenetics Epigenetics Protein Biomarker

Mapping Human Pluripotent Stem Cell-derived Erythroid Differentiation by Single-cell Transcriptome Analysis

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2021年第3期19卷 358-376页

作者： Zijuan Xin Wei Zhang Shangjin Gong Junwei Zhu Yanming Li Zhaojun Zhang xiangdong fang CAS Key Laboralory of Genome Science and Information Beijing Institute of GenomicsChinese Academy of Sciences/China National Center of BioinformationBeijing 100101China College of Life Sciences University of Chinese Academy of SciencesBejing 100049China Sino-Danish College University of Chinese Academy of SciencesBejing 100190.China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China Bejig Key Laboratory of Genome and Precision Medicine Technologies Beijing 100101China

There is an imbalance between the supply and demand of functional red blood cells(RBCs)in clinical *** imbalance can be addressed by regenerating RBCs using several in vitro *** pluripotent stem cells(iPSCs)can handle the low supply of cord blood and the ethical issues in embryonic stem cell research,and provide a promising strategy to eliminate immune ***,no complete single-cell level differentiation pathway exists for the iPSC-derived erythroid differentiation *** this study,we used iPSC line BC1 to establish a RBC regeneration *** 10X Genomics single-cell transcriptome platform was used to map the cell lineage and differentiation trajectory on day 14 of the regeneration *** observed that iPSC differentiation was not synchronized during embryoid body(EB)*** cells(on day 14)mainly consisted of mesodermal and various blood cells,similar to the yolk sac *** identified six cell classifications and characterized the regulatory transcription factor(TF)networks and cell-cell contacts underlying the *** undergo two transformations during the differentiation trajectory,accompanied by the dynamic expression of cell adhesion molecules and estrogen-responsive *** identified erythroid cells at different stages,such as burst-forming unit erythroid(BFU-E)and orthochromatic erythroblast(ortho-E)cells,and found that the regulation of TFs(e.g.,TFDP1 and FOXO3)is erythroid-stage *** erythroid cells were identified in our *** study provides systematic theoretical guidance for optimizing the iPSC-derived erythroid differentiation system,and this system is a useful model for simulating in vivo hematopoietic development and differentiation.

关键词： scRNA-seq iPSC Hematopoiesis Erythropoiesis Differentiation trajectory

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation

在线全文

学校读者我要写书评

暂无评论

Frontiers of Medicine 2016年第3期10卷 297-310页

作者： Nan Ding Jiafei Xi Yanming Li Xiaoyan Xie Jian Shi Zhaojun Zhang Yanhua Li fang fang Sihan Wang Wen Yue Xuetao Pei xiangdong fang CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China Lab of Stem Cell and Regenerative Medicine Beijing Institute of Transfusion Medicine AMMS Beijing 100850 China University of Chinese Academy of Sciences Beijing 100049 China South China Research Center for Stem Cell &Regenerative Medicine AMMS Guangzhou 510300 China

Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and IncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during sternness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heine metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.

关键词： erythroid differentiation hematopoietic stem cell RNA-seq miRNA lncRNA

Biological Databases for Hematology Research

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2016年第6期14卷 333-337页

作者： Qian Zhang Nan Ding Lu Zhang Xuetong Zhao Yadong Yang Hongzhu Qu xiangdong fang CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

With the advances of genome-wide sequencing technologies and bioinformatics approaches, a large number of datasets of normal and malignant erythropoiesis have been gener- ated and made public to researchers around the world. Collection and integration of these datasets greatly facilitate basic research and clinical diagnosis and treatment of blood disorders. Here we provide a brief introduction of the most popular omics data resources of normal and malignant hematopoiesis, including some integrated web tools, to help users get better equipped to perform common analyses. We hope this review will promote the awareness and facilitate the usage of public

关键词： resources in the hematology research.

Gene Regulatory Networks in the Genomics Era

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2013年第3期11卷 133-134页

作者： Matthew Loose Roger Patient xiangdong fang Hongxing Lei1 Institute of Genetics Queen's Medical Centre University of Nottingham The Weatherall Institute of Molecular Medicine John Radcliffe Hospital University of Oxford CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

The precise regulation of gene expression is critical to the nor- mal development and biological function of all organisms. Dysregulation of gene expression during early development can result in a spectrum of failures ranging from minor defects to the termination of development. In adult life, dysregulation can lead to the uncontrolled cell proliferation of cancer or pro- grammed cell death leading to neurodegenerative diseases. The regulation of gene expression is controlled by multiple systems with more being discovered. The immediate regulators are transcription factors which bind to specific sequences in the promoter or enhancer regions of individual genes. The activity of transcription factors can be regulated by the presence of other transcription factors and cofactors, methylation status of the promoter or enhancer region,

关键词： Gene Regulatory Networks in the Genomics Era gene

An RNA-seq-based Gene Expression Profiling of Radiation-induced Tumorigenic Mammary Epithelial Cells

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2012年第6期10卷 326-335页

作者： Lina Ma Linghu Nie Jing Liu Bing Zhang Shuhui Song Min Sun Jin Yang Yadong Yang xiangdong fang Songnian Hu Yongliang Zhao Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Laboratory of Disease Genomics and Individualized Medicine Beijing Institute of Genomics Chinese Academy of Sciences Center for Radiological Research Columbia University

Immortality and tumorigenicity are two distinct characteristics of cancers. Immortalization has been suggested to precede tumorigenesis. To understand the molecular mechanisms of tumorigenicity and cancer progression in mammary epithelium, we established a tumori- genic cell model by means of heavy-ion radiation of an immortal cell model, which was created by overexpressing the human telomerase reverse transcriptase （hTERT） in normal human mammary epithelial cells. We examined the expression profile of this tumorigenic cell line （T hMEC） using the hTERT-overexpressing immortal cell line （IhMEC） as a control. In-depth RNA-seq data was generated by using the next-generation sequencing （NGS） platform （Life Technologies SOLID3）. We found that house-keeping （HK） and tissue-spe- cific （TS） genes were differentially regulated during the tumorigenic process. HK genes tended to be activated while TS genes tended to be repressed. In addition, the HK genes and TS genes tended to contribute differentially to the variation of gene expression at different RPKM （gene expression in reads per exon kilobase per million mapped sequence reads） levels. Based on transcriptome analysis of the two cell lines, we defined 7053 differentially-expressed genes （DEGs） between immortality and tumorigenicity. Differential expression of 20 manually-selected genes was further validated using qRT-PCR. Our observations may help to further our understanding of cellular mechanism（s） in the transition from immortalization to tumorigenesis.

关键词： NGS RNA-seq Tumorigenicity Immortality Radiation Breast cancer