m10kcodGO2ALLPROBES {m10kcod} | R Documentation

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

### Description

m10kcodGO2ALLPROBES is an R environment that provides mappings between a given GO id and all manufactuerer ids 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 ids. The name associated with each manufacturer id corresponds to the evidence code for that GO id. This environment m10kcodGO2ALLPROBES maps between a given GO id and all manufactuerer ids 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 ids. 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 id may be mapped to the same manufacturer id more than once but the evidence code can be different. Mappings between Gene Ontology ids 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 Thu Jun 22 11:38:30 2006

Package built Thu Jun 22 12:05:01 2006

### References

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

### Examples

        # Convert to a list
        xx <- as.list(m10kcodGO2ALLPROBES)
        if(length(xx) > 0){
            # Gets the probe ids for the top 2nd and 3nd GO ids
            goids <- xx[2:3]
            # Gets all the probe ids for the first element of goids
            goids[[1]]
            # Evidence code for the mappings
            names(goids[[1]])
        }

[Package m10kcod version 1.0.0 Index]