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. 2005 Aug 9:6:201.
doi: 10.1186/1471-2105-6-201.

DynGO: a tool for visualizing and mining of Gene Ontology and its associations

Hongfang Liu  1 , Zhang-Zhi Hu, Cathy H Wu
Affiliations

DynGO: a tool for visualizing and mining of Gene Ontology and its associations

Hongfang Liu et al. BMC Bioinformatics. .

Abstract

Background: A large volume of data and information about genes and gene products has been stored in various molecular biology databases. A major challenge for knowledge discovery using these databases is to identify related genes and gene products in disparate databases. The development of Gene Ontology (GO) as a common vocabulary for annotation allows integrated queries across multiple databases and identification of semantically related genes and gene products (i.e., genes and gene products that have similar GO annotations). Meanwhile, dozens of tools have been developed for browsing, mining or editing GO terms, their hierarchical relationships, or their "associated" genes and gene products (i.e., genes and gene products annotated with GO terms). Tools that allow users to directly search and inspect relations among all GO terms and their associated genes and gene products from multiple databases are needed.

Results: We present a standalone package called DynGO, which provides several advanced functionalities in addition to the standard browsing capability of the official GO browsing tool (AmiGO). DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations. The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples.

Conclusion: We have presented a standalone package DynGO that provides functionalities to search and browse GO and its association databases as well as several additional functions such as batch retrieval and semantic retrieval. The complete documentation and software are freely available for download from the website http://biocreative.ifsm.umbc.edu/dyngo.

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Figures

Figure 1
Figure 1
Detection of functional homologs using GO annotations. (a) Sequence alignment based on Smith-Waterman algorithm for YAP1 and JUNB proteins; (b) GO annotations of these two proteins, where the lowest common GO terms in the hierarchies are highlighted based on TAS (Traceable Author Statement) leaf nodes.
Figure 2
Figure 2
An example of tree lifting. (a) RGD-centric view; (b) GO-centric view.
Figure 3
Figure 3
The overall server-client architecture of DynGO.
Figure 4
Figure 4
Screen shots of DynGO. (a) GO tree obtained from all GO terms; (b) Association tree obtained by retrieving products for GO:0015075.
Figure 5
Figure 5
Tree lifting function to dynamically obtain trees with different orientations. (a) Association tree for RGD; (b) View obtained by lifting reference identifiers; (c) View obtained by lifting evidence codes.
Figure 6
Figure 6
Screen shot for exploring association trees. (a) Association tree for all genes in SGD; (b) Relatives of gene SDS24; (c) Annotations for SDS24.
Figure 7
Figure 7
DynGO for the visualization of annotated probe sets for microarray data analysis.
Figure 8
Figure 8
DynGO for the study of complementing GO with the PIRSF protein classification system. (a) Identification of missing GO nodes according to PIRSF families; (b) Linkage of GO sub-ontologies based on PIRSF GO associations.
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