A collection of bioconductor methods to visualize gene-list annotations.
A collection of bioconductor methods to visualize gene-list annotations.
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DOI：
10.1186/1756-0500-3-10
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发表时间：
2010-01-19
影响因子：
1.8
通讯作者：
Lin SM
中科院分区：
文献类型：
--
作者：
Feng G;Du P;Krett NL;Tessel M;Rosen S;Kibbe WA;Lin SM
基因列表注释对于研究人员探索基因和功能之间的复杂关系至关重要。目前，基因列表的注释通常通过表格或条形图来概括。因此，潜在的生物学重要的复杂性，如一个基因属于多个注释类别是难以提取的。我们设计了明确和有效的可视化方法，提供了直观的方法来询问生物类别和基因之间的内在联系。我们已经构建了一个数据模型，现在在Bioconductor包“GeneAnswers”中提出了两种新的方法，以同时可视化基因、概念（也称为“基因”）和基因。注释类别）和概念-基因连接（a.k.a.注释）：“概念和基因网络”和“概念和基因交叉表”。这些方法已被测试和验证与微阵列衍生的基因列表。这些新的可视化方法可以使用基因本体、疾病本体或任何其他用户定义的基因注释来有效地呈现注释，这些注释已经通过人类策展、自动化管道或两者的组合与生物体的基因组预先关联。基因注释数据模型和相关方法可在本出版物中描述的称为“GeneAnswers“的Bioconductor包中获得。
Gene-list annotations are critical for researchers to explore the complex relationships between genes and functionalities. Currently, the annotations of a gene list are usually summarized by a table or a barplot. As such, potentially biologically important complexities such as one gene belonging to multiple annotation categories are difficult to extract. We have devised explicit and efficient visualization methods that provide intuitive methods for interrogating the intrinsic connections between biological categories and genes. We have constructed a data model and now present two novel methods in a Bioconductor package, "GeneAnswers", to simultaneously visualize genes, concepts (a.k.a. annotation categories), and concept-gene connections (a.k.a. annotations): the "Concept-and-Gene Network" and the "Concept-and-Gene Cross Tabulation". These methods have been tested and validated with microarray-derived gene lists. These new visualization methods can effectively present annotations using Gene Ontology, Disease Ontology, or any other user-defined gene annotations that have been pre-associated with an organism's genome by human curation, automated pipelines, or a combination of the two. The gene-annotation data model and associated methods are available in the Bioconductor package called "GeneAnswers " described in this publication.