MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes

Abstract

Gene definitions and identifiers can be painful to manage-more so when trying to include gene function annotations as this can be highly context-dependent. Creating groups of genes or gene sets can help provide such context, but it compounds the issue as each gene within the gene set can map to multiple identifiers and have annotations derived from multiple sources. We developed MyGeneset.info to provide an API for integrated annotations for gene sets suitable for use in analytical pipelines or web servers. Leveraging our previous work with MyGene.info (a server that provides gene-centric annotations and identifiers), MyGeneset.info addresses the challenge of managing gene sets from multiple resources. With our API, users readily have read-only access to gene sets imported from commonly-used resources such as Wikipathways, CTD, Reactome, SMPDB, MSigDB, GO, and DO. In addition to supporting the access and reuse of approximately 180k gene sets from humans, common model organisms (mice, yeast, etc.), and less-common ones (e.g. black cottonwood tree), MyGeneset.info supports user-created gene sets, providing an important means for making gene sets more FAIR. User-created gene sets can serve as a way to store and manage collections for analysis or easy dissemination through a consistent API.

Graphical Abstract

MyGeneset.info provides both programmatic API access and interactive web access to annotated gene sets, either community-curated or user-created.

Figure 1.

Publicly-accessible, curated gene sets are structured as resource plugins in MyGeneset.info, which was built using the BioThings SDK (dotted box). Each plugin retrieves gene annotations from MyGene.info before uploading and merging the data. Users can submit queries via clients or RESTful queries to the API, or via the Vue-based browser interface. Users can build and submit gene sets via the browser interface (dashed arrows).

Figure 2.

The search and browse interface of MyGeneset.info allows users to search for gene sets by keyword (A) or species (B). Users can also search by type (C) including, gene sets generated by the User, publicly accessible Curated gene sets filterable by source, Anonymously submitted gene sets, and All gene sets. The resulting gene set table can be sorted by author, source, and number of genes in the gene set (D). Gene sets can be filtered by the number of genes in the set (E) or by the source (F) if ‘Curated’ is selected in (C).