GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products.
GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products.
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DOI：
10.1186/1471-2105-8-166
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发表时间：
2007-05-22
影响因子：
3
通讯作者：
Beissbarth T
中科院分区：
文献类型：
--
作者：
Fröhlich H;Speer N;Poustka A;Beissbarth T
随着高通量数据（如DNA微阵列数据）可用性的增加，研究人员能够产生大量的生物数据。在分析此类数据时，常常不仅需要进一步探究基因在表达方面的相似性，还需要探究其在可从基因本体论（GO）获得的功能注释方面的相似性。
我们介绍一款免费可用的软件包GOSim，它能够基于基因本体论术语的各种信息论相似性概念来计算基因的功能相似性。GOSim通过为基因提供其他近期开发的功能相似性度量方法，扩展了现有工具。例如，这些方法可用于根据基因的生物学功能对其进行聚类。反之，它们也可用于评估给定基因分组在基因本体论注释方面的同质性。因此，GOSim为研究人员提供了一个灵活且强大的工具，将基因本体论中存储的知识与实验数据相结合。它可被视为对其他工具的补充，例如那些在给定基因组中搜索显著过度表达的基因本体论术语的工具。
GOSim是作为统计计算环境R的一个软件包来实现的，并在CRAN项目中遵循通用公共许可证（GPL）发布。
With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the need to further explore the similarity of genes not only with respect to their expression, but also with respect to their functional annotation which can be obtained from Gene Ontology (GO). We present the freely available software package GOSim, which allows to calculate the functional similarity of genes based on various information theoretic similarity concepts for GO terms. GOSim extends existing tools by providing additional lately developed functional similarity measures for genes. These can e.g. be used to cluster genes according to their biological function. Vice versa, they can also be used to evaluate the homogeneity of a given grouping of genes with respect to their GO annotation. GOSim hence provides the researcher with a flexible and powerful tool to combine knowledge stored in GO with experimental data. It can be seen as complementary to other tools that, for instance, search for significantly overrepresented GO terms within a given group of genes. GOSim is implemented as a package for the statistical computing environment R and is distributed under GPL within the CRAN project.
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影响因子：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R
影响因子：
5.8
作者：
Beissbarth, T;Speed, TP
通讯作者：
Speed, TP
DOI：
10.1016/0377-0427(87)90125-7
发表时间：
1987-11-01
影响因子：
2.4
作者：
ROUSSEEUW, PJ
通讯作者：
ROUSSEEUW, PJ
影响因子：
5
作者：
Resnik, P
通讯作者：
Resnik, P
DOI：
10.1073/pnas.95.25.14863
发表时间：
1998-12-08
影响因子：
11.1
作者：
Eisen, MB;Spellman, PT;Botstein, D
通讯作者：
Botstein, D