Overview of the HCGene R package

The R package HCGene (Hierarchical Classification of Genes) implements methods to process and analyze the Gene Ontology (GO) [6] and the FunCat [10] taxonomy in order to support the functional classification of genes.

GO and FunCat encode binary relations among functional classes. The graph induced on the class nodes by these relations is a DAG (directed acyclic graph) for the Gene Ontology and a tree for FunCat. Annotations for genes and gene products are provided for both hierarchies at different degrees of resolution and reliability, and involve multiple classes.

We can divide the pre-processing of data and classes in three main logical steps.

Processing of functional classes of genes: Analysis of the characteristics of GO graphs and FunCat trees, and extraction of subgraphs related to the problem under investigation.
Labeling gene products with functional classes: Association of multiple GO or FunCat classes to gene products.
Association of gene products to data: Association of the gene products to their corresponding biological data (e.g., gene expression data, phylogenetic or protein-protein interaction data).

The HCGene R package provides methods and functionalities to support all of the above steps. Moreover, it allows to analyze the properties of GO graphs and FunCat trees associated to both human and specific model organisms (such as S. cerevisiae, Mus musculus and Arabidopsis thaliana). Methods for computing various statistics on the structure of GO and FunCat, and their associated gene products are also included in the library.

To download the R software and documentation (including the reference manual in pdf format) go to section Download software and documentation.

The other sections provide a brief introduction to: the functional classification of genes with GO and FunCat, a presentation of the main functionalities of the library, and two practical examples of usage of the HCGene library: