2012年盘基网柄菌的一站式服务平台：盘基网柄菌数据库和盘基网柄菌菌种保藏中心
One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.
作者信息
Fey Petra, Dodson Robert J, Basu Siddhartha, Chisholm Rex L
机构信息
dictyBase and the Dicty Stock Center, Center for Genetic Medicine, Northwestern University, Chicago, IL, USA.
出版信息
Methods Mol Biol. 2013;983:59-92. doi: 10.1007/978-1-62703-302-2_4.
Abstract
dictyBase (http://dictybase.org), the model organism database for Dictyostelium discoideum, includes the complete genome sequence and expression data for this organism. Relevant literature is integrated into the database, and gene models and functional annotation are manually curated from experimental results and comparative multigenome analyses. dictyBase has recently expanded to include the genome sequences of three additional Dictyostelids and has added new software tools to facilitate multigenome comparisons. The Dicty Stock Center, a strain and plasmid repository for Dictyostelium research, has relocated to Northwestern University in 2009. This allowed us integrating all Dictyostelium resources to better serve the research community. In this chapter, we will describe how to navigate the Web site and highlight some of our newer improvements.
相似文献
1
One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.2012年盘基网柄菌的一站式服务平台：盘基网柄菌数据库和盘基网柄菌菌种保藏中心
Methods Mol Biol. 2013;983:59-92. doi: 10.1007/978-1-62703-302-2_4.
2
dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa.dictyBase 2011年更新：Web 2.0功能以及迈向变形虫基因组门户的初步步骤。
Nucleic Acids Res. 2011 Jan;39(Database issue):D620-4. doi: 10.1093/nar/gkq1103. Epub 2010 Nov 17.
3
dictyBase, the model organism database for Dictyostelium discoideum.盘基网柄菌模式生物数据库（dictyBase），用于盘基网柄菌。
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D423-7. doi: 10.1093/nar/gkj090.
4
dictyBase and the Dicty Stock Center.盘基网柄菌数据库和盘基网柄菌菌种保藏中心。
Methods Mol Biol. 2006;346:51-74. doi: 10.1385/1-59745-144-4:51.
5
DictyBase 2013: integrating multiple Dictyostelid species.DictyBase 2013：整合多个盘基网柄菌物种。
Nucleic Acids Res. 2013 Jan;41(Database issue):D676-83. doi: 10.1093/nar/gks1064. Epub 2012 Nov 20.
6
dictyBase and the Dicty Stock Center (version 2.0) - a progress report.盘基网柄菌数据库与盘基网柄菌菌种保藏中心（2.0版）——进展报告
Int J Dev Biol. 2019;63(8-9-10):563-572. doi: 10.1387/ijdb.190226pf.
7
dictyBase 2015: Expanding data and annotations in a new software environment.dictyBase 2015：在新软件环境中扩展数据与注释
Genesis. 2015 Aug;53(8):523-534. doi: 10.1002/dvg.22867. Epub 2015 Jul 8.
8
dictyBase--a Dictyostelium bioinformatics resource update.dictyBase——一种盘基网柄菌生物信息学资源更新
Nucleic Acids Res. 2009 Jan;37(Database issue):D515-9. doi: 10.1093/nar/gkn844. Epub 2008 Oct 30.
9
dictyBase: a new Dictyostelium discoideum genome database.dictyBase：一个新的盘基网柄菌基因组数据库。
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D332-3. doi: 10.1093/nar/gkh138.
10
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR.生物注释工作流程中的文本挖掘：在 WormBase、dictyBase 和 TAIR 中进行文献注释的应用。
Database (Oxford). 2012 Nov 17;2012:bas040. doi: 10.1093/database/bas040. Print 2012.
引用本文的文献
1
Myosin 2 drives actin contractility in fast-crawling species outside of the amorphean lineage.肌球蛋白2在无变形虫谱系之外的快速爬行物种中驱动肌动蛋白收缩。
bioRxiv. 2025 May 19:2025.05.16.654244. doi: 10.1101/2025.05.16.654244.
2
Two endogenous chemorepellents use different mechanisms to induce repulsion.两种内源性化学排斥剂通过不同机制诱导排斥反应。
Proc Natl Acad Sci U S A. 2025 Jun 3;122(22):e2503168122. doi: 10.1073/pnas.2503168122. Epub 2025 May 27.
3
Luminal Phospholipase D Attacks Bacterial Membranes in Dictyostelium discoideum Phagosomes.管腔磷脂酶D攻击盘基网柄菌吞噬体中的细菌膜。
Mol Microbiol. 2025 Jul;124(1):54-65. doi: 10.1111/mmi.15367. Epub 2025 May 4.
4
MAST Kinases' Function and Regulation: Insights from Structural Modeling and Disease Mutations.MAST激酶的功能与调控：来自结构建模和疾病突变的见解
Biomedicines. 2025 Apr 9;13(4):925. doi: 10.3390/biomedicines13040925.
5
Tubulin sequence divergence is associated with the use of distinct microtubule regulators.微管蛋白序列差异与不同微管调节因子的使用有关。
Curr Biol. 2025 Jan 20;35(2):233-248.e8. doi: 10.1016/j.cub.2024.11.022. Epub 2024 Dec 17.
6
APEX2-Mediated Proximity Protein Labeling in Dictyostelium.APEX2 介导的盘基网柄菌邻近蛋白标记。
Methods Mol Biol. 2024;2814:119-131. doi: 10.1007/978-1-0716-3894-1_9.
7
Polycystin-2 Mediated Calcium Signalling in the Model for Autosomal Dominant Polycystic Kidney Disease.多囊蛋白-2 介导的常染色体显性遗传多囊肾病模型中的钙信号转导。
Cells. 2024 Mar 31;13(7):610. doi: 10.3390/cells13070610.
8
An integrated, cross-regulation pathway model involving activating/adaptive and feed-forward/feed-back loops for directed oscillatory cAMP signal-relay/response during the development of .在……发育过程中，一个涉及激活/适应性以及前馈/反馈回路的整合交叉调节通路模型，用于定向振荡性环磷酸腺苷（cAMP）信号中继/响应 。 （注：原文句子不完整，“during the development of”后面缺少具体内容）
Front Cell Dev Biol. 2024 Jan 31;11:1263316. doi: 10.3389/fcell.2023.1263316. eCollection 2023.
9
A dynamic partitioning mechanism polarizes membrane protein distribution.动态分区机制使膜蛋白分布极化。
Nat Commun. 2023 Nov 30;14(1):7909. doi: 10.1038/s41467-023-43615-2.
10
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.2024 年的“君主计划”：一个整合跨物种表型、基因和疾病的分析平台。
Nucleic Acids Res. 2024 Jan 5;52(D1):D938-D949. doi: 10.1093/nar/gkad1082.
本文引用的文献
1
GenBank.GenBank。
Nucleic Acids Res. 2012 Jan;40(Database issue):D48-53. doi: 10.1093/nar/gkr1202. Epub 2011 Dec 5.
2
The Pfam protein families database.Pfam 蛋白质家族数据库。
Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301. doi: 10.1093/nar/gkr1065. Epub 2011 Nov 29.
3
The Proteome Folding Project: proteome-scale prediction of structure and function.蛋白质组折叠计划：蛋白质组规模的结构和功能预测。
Genome Res. 2011 Nov;21(11):1981-94. doi: 10.1101/gr.121475.111. Epub 2011 Aug 8.
4
Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication.全基因组进化分析揭示了复杂细胞间通讯的古老起源。
Genome Res. 2011 Nov;21(11):1882-91. doi: 10.1101/gr.121137.111. Epub 2011 Jul 14.
5
UniProt Knowledgebase: a hub of integrated protein data.UniProt 知识库：一个集成蛋白质数据的中心。
Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011.
6
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.黏菌的社会阿米巴 Dictyostelium discoideum 和 Dictyostelium purpureum 的比较基因组学。
Genome Biol. 2011;12(2):R20. doi: 10.1186/gb-2011-12-2-r20. Epub 2011 Feb 28.
7
The what, where, how and why of gene ontology--a primer for bioinformaticians.基因本体论的是什么、在哪里、如何以及为什么——生物信息学家入门。
Brief Bioinform. 2011 Nov;12(6):723-35. doi: 10.1093/bib/bbr002. Epub 2011 Feb 17.
8
dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa.dictyBase 2011年更新：Web 2.0功能以及迈向变形虫基因组门户的初步步骤。
Nucleic Acids Res. 2011 Jan;39(Database issue):D620-4. doi: 10.1093/nar/gkq1103. Epub 2010 Nov 17.
9
The European Nucleotide Archive.欧洲核苷酸数据库。
Nucleic Acids Res. 2011 Jan;39(Database issue):D28-31. doi: 10.1093/nar/gkq967. Epub 2010 Oct 23.
10
Conserved developmental transcriptomes in evolutionarily divergent species.进化上差异较大的物种中保守的发育转录组。
Genome Biol. 2010;11(3):R35. doi: 10.1186/gb-2010-11-3-r35. Epub 2010 Mar 17.
Zotero 插件