BABELOMICS：基因组规模实验功能注释中的系统生物学视角。
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
作者信息
Al-Shahrour Fátima, Minguez Pablo, Tárraga Joaquín, Montaner David, Alloza Eva, Vaquerizas Juan M, Conde Lucía, Blaschke Christian, Vera Javier, Dopazo Joaquín
机构信息
Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, E-46013, Valencia, Spain.
出版信息
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6. doi: 10.1093/nar/gkl172.
Abstract
We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at http://www.babelomics.org.
摘要
我们展示了Babelomics的新版本，这是一套用于基因组规模实验功能分析的完整网络工具集，并配备了全新且经过改进的工具。新纳入了一些功能相关的术语，如顺式作用元件基序或通过文本挖掘程序获得的生物实体。改进后的索引显著加快了几个模块的运行速度。我们还展示了用于研究功能相关基因组协同行为的FatiScan方法的改进版本，以及类似工具基因集富集分析。Babelomics现在更侧重于检验受系统生物学启发的假设。可通过http://www.babelomics.org访问Babelomics。
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本文引用的文献
1
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Drug Discov Today. 2006 Apr;11(7-8):315-25. doi: 10.1016/j.drudis.2006.02.011.
2
Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.基于转录因子结合亲和力分析的哺乳动物增强子全基因组预测
Cell. 2006 Jan 13;124(1):47-59. doi: 10.1016/j.cell.2005.10.042.
3
cisRED: a database system for genome-scale computational discovery of regulatory elements.cisRED：一个用于全基因组规模计算发现调控元件的数据库系统。
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D68-73. doi: 10.1093/nar/gkj075.
4
The Universal Protein Resource (UniProt): an expanding universe of protein information.通用蛋白质资源（UniProt）：不断扩展的蛋白质信息宇宙。
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5
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.基因集富集分析：一种基于知识的方法用于解读全基因组表达谱。
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. doi: 10.1073/pnas.0506580102. Epub 2005 Sep 30.
6
Towards a proteome-scale map of the human protein-protein interaction network.迈向人类蛋白质-蛋白质相互作用网络的蛋白质组规模图谱。
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7
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