hwgcodGO2ALLPROBES {hwgcod} | R Documentation

## Map Between Gene Ontology (GO) Identifiers and all Manufacturer Identifiers in the subtree

### Description

hwgcodGO2ALLPROBES is an R environment that provides mappings between a given GO identifier and all manufactuerer identifiers annotated at that GO term or one of its children in the GO ontology.

### Details

GO consists of three ontologies—molecular function (MF), biological process (BP), and cellular component (CC). All ontologies are structured as directed acyclic graphs (DAGs). Each node in each DAG (tree) is a GO term (id) associated with a named vector of manufacturer identifiers. The name associated with each manufacturer id corresponds to the evidence code for that GO identifier. This environment hwgcodGO2ALLPROBES maps between a given GO identifier and all manufactuerer identifiers annotated at that GO term or one of its children in the GO ontology.

The evidence code indicates what kind of evidence supports the association between the GO and Entrez Gene identifiers. Evidence codes currently in use include:

IMP - inferred from mutant phenotype

IGI - inferred from genetic interaction

IPI - inferred from physical interaction

ISS - inferred from sequence similarity

IDA - inferred from direct assay

IEP - inferred from expression pattern

IEA - inferred from electronic annotation

TAS - traceable author statement

NAS - non-traceable author statement

ND - no biological data available

IC - inferred by curator

A GO identifier may be mapped to the same manufacturer identifier more than once but the evidence code can be different. Mappings between Gene Ontology identifiers and Gene Ontology terms and other information are available in a separate data package named GO.

Mappings were based on data provided by:

Entrez Gene:ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/. Built: Source data downloaded from Entrez Gene on Fri Sep 8 20:40:53 2006

Package built Fri Sep 8 21:43:54 2006

### References

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

### Examples

        # Convert to a list
        xx <- as.list(hwgcodGO2ALLPROBES)
        if(length(xx) > 0){
            # Gets the probe identifiers for the top 2nd and 3nd GO identifiers
            goids <- xx[2:3]
            # Gets all the probe identifiers for the first element of goids
            goids[[1]]
            # Evidence code for the mappings
            names(goids[[1]])
        }

[Package hwgcod version 1.2.0 Index]