GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms

Smid M; Dorssers LCJ

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GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms

机译：GO-Mapper：使用表达水平作为评分来评估基因本体论术语的基因表达数据的功能分析

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Motivation: Retrieval of information on biological processes from large-scale expression data is still a time-consuming task. An automated analysis utilizing all expression information would greatly increase our understanding of the samples under study.Results: We describe here a novel method to obtain a functional analysis of complex gene expression data. Instead of applying a predefined expression threshold, Gene Ontology (GO) terms are weighted using the actual measured levels of expression of all associated genes. Based on this concept, the application GO-Mapper was developed to quantitatively link gene expression levels to GO-terms for multiple experiments in an automated way. The applicability of GO-Mapper was developed and validated on in house and public human microarray data and mouse SAGE data. We demonstrate that the GO-Mapper allows for interrelating relevant biological functions with the experiments under study.

机译：动机：从大规模表达数据中检索生物过程信息仍然是一项耗时的任务。利用所有表达信息的自动分析将大大提高我们对所研究样品的了解。结果：在此我们描述了一种获得复杂基因表达数据功能分析的新方法。代替应用预定义的表达阈值，使用所有相关基因的实际表达水平对基因本体论（GO）术语进行加权。基于此概念，开发了应用程序GO-Mapper，以自动方式将基因表达水平与GO术语定量连接，以进行多个实验。 GO-Mapper的适用性是在室内和公共人类微阵列数据和小鼠SAGE数据上开发和验证的。我们证明GO-Mapper可以使相关的生物学功能与正在研究的实验相互关联。

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来源
《Bioinformatics》 |2004年第16期|p. 2618-2625|共8页
作者
Smid M; Dorssers LCJ;
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作者单位

Erasmus MC, Josephine Nefkens Inst, Dept Pathol, NL-3000 DR Rotterdam, Netherlands;

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收录信息美国《科学引文索引》(SCI);美国《化学文摘》(CA);
原文格式 PDF
正文语种 eng
中图分类生物科学;
关键词
SERIAL ANALYSIS; MICROARRAY DATA; RESOURCE; GENOME; TOOL;

机译：序列分析;微阵列数据;资源;基因组;工具;

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专利

1. GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms [J] . Smid M, Dorssers LCJ Bioinformatics . 2004,第16期

机译：GO-Mapper：使用表达水平作为评分来评估基因本体论术语的基因表达数据的功能分析
2. Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. [J] . Brameier M, Wiuf C Journal of biomedical informatics. . 2007,第2期

机译：使用自组织图谱对酿酒酵母的基因表达数据和基因本体术语进行共聚和可视化。
3. Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. [J] . Ozaki S, Ogata Y, Suda K, DNA research: an international journal for rapid publication of reports on genes and genomes . 2010,第2期

机译：番茄基因的共表达分析和在功能丰富的共表达模块中发现的基因协调表达的实验验证。
4. Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data [C] . Pramod K. Gupta, Ryo Yoshida, Seiya Imoto, Bioinformatics Research and Applications; Lecture Notes in Bioinformatics; 4463 . 2007

机译：具有基因表达数据的基因本体术语的统计绝对评估
5. Functional analysis of cell cycle genes by genome-wide expression data and meta-analysis of RNAi screens. [D] . George, Lacy K. 2010

机译：通过全基因组表达数据和RNAi筛查的荟萃分析对细胞周期基因进行功能分析。
6. GOFFA: Gene Ontology For Functional Analysis – A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data [O] . Hongmei Sun, Hong Fang, Tao Chen, 2006

机译：GOFFA：用于功能分析的基因本体–用于分析基因组和蛋白质组数据的FDA基因本体工具
7. GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms [O] . M. Smid, L. C. J. Dorssers 2004

机译：Go-Mapper：使用表达水平作为评分的基因表达数据的功能分析，以评估基因本体论术语
8. ERG Expression Levels in Prostate Tumors Reflect Functional Status of the Androgen Receptor (AR) as a Consequence of Fusion of ERG with AR Regulated Gene Promoters [R] . 2010

机译：前列腺肿瘤中ERG表达水平反映雄激素受体（aR）的功能状态，作为ERG与aR调节基因启动子融合的后果

GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms

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