DOSim: an R package for similarity between diseases based on Disease Ontology.
DOSim: an R package for similarity between diseases based on Disease Ontology.
复制标题
DOSim：基于疾病本体论的疾病相似性 R 包
DOI：
10.1186/1471-2105-12-266
复制
发表时间：
2011-06-29
影响因子：
3
通讯作者：
Li X
中科院分区：
文献类型：
--
作者：
Li J;Gong B;Chen X;Liu T;Wu C;Zhang F;Li C;Li X;Rao S;Li X
疾病本体（DO）的构建促进了对疾病和疾病危险因素的研究。DO使研究人员能够通过采用语义相似性度量来分析疾病相似性，并扩展了我们对不同疾病之间关系的理解并对其进行分类。同时，基因之间的相似性也可以通过它们与类似疾病的关联来分析。因此，疾病异质性得到了更好的理解，并对类似疾病的分子发病机制有了更深入的了解。然而，生物信息学工具，提供简单和直接的方法使用DO来研究疾病和基因相似性同时是必需的。结果我们开发了一个基于r语言的软件包（DOSim）来计算疾病之间的相似度，并测量人类基因在疾病方面的相似度。DOSim包含基于do的富集分析功能，可用于探索独立基因集的疾病特征。多层富集分析（GO和KEGG注释）注释功能，帮助用户探索新检测到的基因模块所隐含的生物学意义，也是DOSim包的一部分。我们使用疾病相似度应用程序来演示128种不同DO癌症术语之间的关系。这128种不同癌症的分层聚类显示出模块化特征。在另一个案例研究中，我们对361个肥胖相关基因使用了基因相似性应用。结果揭示了肥胖的复杂发病机制。此外，将DOSim中的基因模块检测和基因模块多层注释功能应用于这361个肥胖相关基因，有助于我们进一步了解肥胖风险表型的复杂发病机制和肥胖相关疾病的异质性。结论sdosim可用于检测疾病驱动基因模块，并对这些模块的功能和通路进行标注。DOSim包也可以用来可视化DO结构。DOSim可以反映疾病相关基因的模块化特征，促进我们对疾病复杂发病机制的认识。DOSim可在综合R档案网络（CRAN）或http://bioinfo.hrbmu.edu.cn/dosim上获得。
BackgroundThe construction of the Disease Ontology (DO) has helped promote the investigation of diseases and disease risk factors. DO enables researchers to analyse disease similarity by adopting semantic similarity measures, and has expanded our understanding of the relationships between different diseases and to classify them. Simultaneously, similarities between genes can also be analysed by their associations with similar diseases. As a result, disease heterogeneity is better understood and insights into the molecular pathogenesis of similar diseases have been gained. However, bioinformatics tools that provide easy and straight forward ways to use DO to study disease and gene similarity simultaneously are required.ResultsWe have developed an R-based software package (DOSim) to compute the similarity between diseases and to measure the similarity between human genes in terms of diseases. DOSim incorporates a DO-based enrichment analysis function that can be used to explore the disease feature of an independent gene set. A multilayered enrichment analysis (GO and KEGG annotation) annotation function that helps users explore the biological meaning implied in a newly detected gene module is also part of the DOSim package. We used the disease similarity application to demonstrate the relationship between 128 different DO cancer terms. The hierarchical clustering of these 128 different cancers showed modular characteristics. In another case study, we used the gene similarity application on 361 obesity-related genes. The results revealed the complex pathogenesis of obesity. In addition, the gene module detection and gene module multilayered annotation functions in DOSim when applied on these 361 obesity-related genes helped extend our understanding of the complex pathogenesis of obesity risk phenotypes and the heterogeneity of obesity-related diseases.ConclusionsDOSim can be used to detect disease-driven gene modules, and to annotate the modules for functions and pathways. The DOSim package can also be used to visualise DO structure. DOSim can reflect the modular characteristic of disease related genes and promote our understanding of the complex pathogenesis of diseases. DOSim is available on the Comprehensive R Archive Network (CRAN) or http://bioinfo.hrbmu.edu.cn/dosim .
登录
查看更多内容
DOI：
10.1093/bioinformatics/btp193
发表时间：
2009-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Du P;Feng G;Flatow J;Song J;Holko M;Kibbe WA;Lin SM
通讯作者：
Lin SM
影响因子：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R
影响因子：
3
作者：
Fröhlich H;Speer N;Poustka A;Beissbarth T
通讯作者：
Beissbarth T
Mendelian在人类及其在线版本中的继承Omim。
影响因子：
9.8
作者：
McKusick, Victor A.
通讯作者：
McKusick, Victor A.
SubpathwayMiner：灵活识别路径的软件包
影响因子：
14.9
作者：
Li C;Li X;Miao Y;Wang Q;Jiang W;Xu C;Li J;Han J;Zhang F;Gong B;Xu L
通讯作者：
Xu L