A collection of bioconductor methods to visualize gene-list annotations

Abstract

Background: 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.

Findings: 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.

Conclusions: 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.

Figure 1

Distribution of statistical significance on selected GO categories. P-values were calculated from the hypergeometric test. The number of genes in each category is also listed.

Figure 2

Concept-and-gene network. Green and red solid circles represent down and up regulation of genes, respectively. Yellow solid circles stand for the given GO categories. The size of each yellow dot is proportional to the statistical significance of the identified genes in corresponding GO categories.

Figure 3

Concept-and-gene cross tabulations. The left side is a heatmap in which green and red bars represent lower and higher expression based on the gene expression profile, respectively. The right side is the annotation table, which shows the relationship between genes and six relevant GO categories. Ctrl: control; Trt24: treatment after 24 hours.