Gavin2006BPGraph {ppiData} | R Documentation

## A directed Graph for the AP-MS Bait to Prey Interaction data detected by Gavin et al. 2006.

### Description

An instance of class graph, Gavin2006BPGraph 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. 2006. 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.

The data from Gavin et al. 2006 were obtained via the Intact repository. The Intact repository assigns an Intact specific code for each VB and each VP. Each Intact ID is mapped to the a SGD ID (if available) and then mapped to the gene systematic name via the YEASTCOMMON2SYSTEMATIC environment of the YEAST R-data package. If the mapping is one to many at any point, the first entry of the mapping is selected. While this selection is arbitrary, there is no definitive way to select from the mappings without more information. If more information concerning the experiment is given, the non-arbitrary choice can be made.

For example: x –> (a,b); a –> (c,d); b –> (e,f), in our algorithm, x ——-> c

If no proper mapping could be achieved in this manner, the Intact ID's were kept so that other methods can be employed for translation in the future. In all 3 VBs and 8 VPs could not be mapped to the gene systematic names.

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(Gavin2006BPGraph)

### Format

The format is: graphNEL "Gavin2006BPGraph"

### Source

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

### References

Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006 Mar 30;440(7084):631-6. Epub 2006 Jan 22.

### Examples

    data(Gavin2006BPGraph)

[Package ppiData version 0.0.8 Index]