Abstract
BackgroundA 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.ResultsWe 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.ConclusionWe 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 .
Highlights
A large amount of data and information about genes and gene products has been stored in various molecular biology databases
The retrieval of genes and gene products across multiple databases that are semantically related to a query gene or gene product allows users to investigate functional relationships among them
We present the semantic similarity of Gene Ontology (GO), which is used by DynGO for semantic retrieval
Summary
A large volume of data and information about genes and gene products has been stored in various molecular biology 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). To assist with the representation and integration of knowledge about genes and gene products, biological ontologies and tools have been developed One such ontology is the Gene Ontology (GO) [1], which has become a major vocabulary for annotating genes and gene (page number not for citation purposes). The yeast YAP1 protein (YAP1_YEAST, 650aa) and the human Jun-B protein (JUNB_HUMAN, 347aa) share little sequence similarity (30% sequence identity in 53aa overlapped region) (Figure 1a) Their functional relationship is revealed by their associated GO annotations, which indicate that both are involved in transcription (GO:0006350), DNA binding (GO:0003677) and transcription regulator activity (GO:0030528).
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