Gavin2002BPGraph {ppiData} | R Documentation

## A directed Graph for the AP-MS Bait to Prey Interaction data detected by Gavin et al. 2002.

### Description

An instance of class graph, Gavin2002BPGraph is a graphNEL object. The nodes are the union of viable baits (VB) and viable prey (VP) of the experiment conducted by Gavin et al. 2002. A viable bait is a node that has at least one directed edge for which this node serves as the source. A viable prey is a node that has at least one directed edge for which this node serves as a sink.

One key fact is that Gavin et al. Used the protein common names when they recorded the data. As we have chosen to use the gene systematic names, we had to map from these common names to systematic names. We used the org.Sc.sgdCOMMON2ORF environment of the org.Sc.sgd R-data package to translate from common protein names to systematic gene names.

We encountered two mappings which were not one to one. The VPs "Osh1" and "Swh1" both mapped to the Open Reading Frame (ORF) "YAR042W". The VPs "Blm3" and the alias "YFL006W" both mapped to the ORF "YFL007W". When mappings are not one to one, it is difficult to reproduce all the information.

The VPs "Osh1" and "Swh1" were found by the same VB "Scs2" while "Blm3" and the alias "YFL006W" were both detected by the VB "Scl1". In creating this graphNEL, we deleted the VPs "Swh1" and "YFL006W".

If, on the other hand, one protein mapped to several different ORFs we simple selected the first ORF in the list since there is no definitive process to make the choice un-arbitrary.

For example: x –> (a,b), then x —> a in our algorithm.

These graphs are not simple. While we chose not to present data with multiple edges between nodes (i.e. if bait b found prey p with multiplicity k, we do not assign k directed edges from b to p, only a single edge). We do, however, allow self loops to detail homodimer relationships.

### Usage

    data(Gavin2002BPGraph)

### Format

The format is: graphNEL "Gavin2002BPGraph"

### Source

The adjacency matrix for this graph can be found in the bioconductor R-package apComplex.

### References

Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002 Jan 10;415(6868):141-7

### Examples

    data(Gavin2002BPGraph)

[Package ppiData version 0.1.13 Index]