Building an ENCODE-style data compendium on a shoestring.
作者信息
Ruau David, Ng Felicia S L, Wilson Nicola K, Hannah Rebecca, Diamanti Evangelia, Lombard Patrick, Woodhouse Steven, Göttgens Berthold
机构信息
1] Department of Hematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK. [2] Wellcome Trust-Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
出版信息
Nat Methods. 2013 Oct;10(10):926. doi: 10.1038/nmeth.2643.
Abstract
摘要
相似文献
1
Building an ENCODE-style data compendium on a shoestring.用极少的资金构建一个类似ENCODE计划的数据汇编。
Nat Methods. 2013 Oct;10(10):926. doi: 10.1038/nmeth.2643.
2
ENCODE whole-genome data in the UCSC Genome Browser: update 2012.在 UCSC Genome Browser 中对全基因组数据进行编码：2012 年更新。
Nucleic Acids Res. 2012 Jan;40(Database issue):D912-7. doi: 10.1093/nar/gkr1012. Epub 2011 Nov 9.
3
An encyclopedia of mouse DNA elements (Mouse ENCODE).小鼠DNA元件百科全书（小鼠ENCODE）。
Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.
4
Generating Publication-Ready Prokaryotic Genome Annotations with DFAST.使用DFAST生成可用于发表的原核生物基因组注释。
Methods Mol Biol. 2019;1962:215-226. doi: 10.1007/978-1-4939-9173-0_13.
5
EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive.EMBLmyGFF3：一种便于向欧洲核苷酸档案库提交基因组注释的转换器。
BMC Res Notes. 2018 Aug 13;11(1):584. doi: 10.1186/s13104-018-3686-x.
6
SNPedia: a wiki supporting personal genome annotation, interpretation and analysis.SNPedia：一个支持个人基因组注释、解释和分析的维基。
Nucleic Acids Res. 2012 Jan;40(Database issue):D1308-12. doi: 10.1093/nar/gkr798. Epub 2011 Dec 2.
7
The Ensembl gene annotation system.Ensembl基因注释系统。
Database (Oxford). 2016 Jun 23;2016. doi: 10.1093/database/baw093. Print 2016.
8
The Ensembl Variant Effect Predictor.Ensembl变异效应预测器。
Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4.
9
ENCODE whole-genome data in the UCSC Genome Browser.在 UCSC 基因组浏览器中对全基因组数据进行编码。
Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. doi: 10.1093/nar/gkp961. Epub 2009 Nov 17.
10
The UCSC Genome Browser database: 2015 update.加州大学圣克鲁兹分校基因组浏览器数据库：2015年更新
Nucleic Acids Res. 2015 Jan;43(Database issue):D670-81. doi: 10.1093/nar/gku1177. Epub 2014 Nov 26.
引用本文的文献
1
Unveiling the complexity of transcription factor networks in hematopoietic stem cells: implications for cell therapy and hematological malignancies.揭示造血干细胞中转录因子网络的复杂性：对细胞治疗和血液系统恶性肿瘤的影响。
Front Oncol. 2023 Jun 27;13:1151343. doi: 10.3389/fonc.2023.1151343. eCollection 2023.
2
Stems cells, big data and compendium-based analyses for identifying cell types, signalling pathways and gene regulatory networks.用于识别细胞类型、信号通路和基因调控网络的干细胞、大数据及基于纲要的分析。
Biophys Rev. 2019 Feb;11(1):41-50. doi: 10.1007/s12551-018-0486-4. Epub 2019 Jan 25.
3
A graphical model approach visualizes regulatory relationships between genome-wide transcription factor binding profiles.图形模型方法直观地展示了全基因组转录因子结合谱之间的调控关系。
Brief Bioinform. 2018 Jan 1;19(1):162-173. doi: 10.1093/bib/bbw102.
4
DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias.DNMT3A缺失导致FLT3-ITD相关白血病中的增强子低甲基化。
Cancer Cell. 2016 Jun 13;29(6):922-934. doi: 10.1016/j.ccell.2016.05.003.
5
ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites.ConBind：用于识别功能性转录因子结合位点的基序感知跨物种比对
Nucleic Acids Res. 2016 May 5;44(8):e72. doi: 10.1093/nar/gkv1518. Epub 2015 Dec 31.
6
SBR-Blood: systems biology repository for hematopoietic cells.SBR-血液：造血细胞的系统生物学知识库。
Nucleic Acids Res. 2016 Jan 4;44(D1):D925-31. doi: 10.1093/nar/gkv1263. Epub 2015 Nov 20.
7
Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.受限的转录因子间距普遍存在且对小鼠血细胞的转录调控很重要。
Nucleic Acids Res. 2014 Dec 16;42(22):13513-24. doi: 10.1093/nar/gku1254. Epub 2014 Nov 26.
8
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities.CODEX：一个面向造血干细胞和胚胎干细胞领域的新一代测序实验数据库。
Nucleic Acids Res. 2015 Jan;43(Database issue):D1117-23. doi: 10.1093/nar/gku895. Epub 2014 Sep 30.
9
Transcriptional network control of normal and leukaemic haematopoiesis.正常和白血病造血的转录网络控制
Exp Cell Res. 2014 Dec 10;329(2):255-64. doi: 10.1016/j.yexcr.2014.06.021. Epub 2014 Jul 8.
10
Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points.造血转录机制：从特定基因座到全基因组的视角。
Exp Hematol. 2014 Aug;42(8):618-29. doi: 10.1016/j.exphem.2014.05.004. Epub 2014 May 9.
本文引用的文献
1
Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data.基因集调控分析预测了从全基因组转录因子结合数据中造血的调控机制。
Exp Hematol. 2013 Apr;41(4):354-66.e14. doi: 10.1016/j.exphem.2012.11.008. Epub 2012 Dec 4.
2
The end of "small science"?“小科学”的终结？
Science. 2012 Sep 28;337(6102):1583. doi: 10.1126/science.1230529.
3
Model-based analysis of ChIP-Seq (MACS).基于模型的染色质免疫沉淀测序分析（MACS）
Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17.
4
Creation and implications of a phenome-genome network.表型组-基因组网络的构建及其意义
Nat Biotechnol. 2006 Jan;24(1):55-62. doi: 10.1038/nbt1150.
Zotero 插件