ItoCore2001BPGraph {ppiData} | R Documentation

## A directed Graph for the Y2H Bait to Prey Interaction data detected by Ito et al. 2001.

### Description

An instance of class graph, ItoCore2001BPGraph is a graphNEL object. The nodes are the union of viable baits (VB) and viable prey (VP) of the experiment conducted by Ito et al. 2001 which they annotated as the core dataset by having verified the bait-prey interaction at least 3 times. 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 Ito et al. 2001 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 7 VBs and 12 VPs could not be mapped to the gene systematic names, and so retain the Intact ID's.

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(ItoCore2001BPGraph)

### Format

The format is: graphNEL "ItoCore2001BPGraph"

### Source

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

### References

A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4569-74. Epub 2001 Mar 13.

### Examples

    data(ItoCore2001BPGraph)

[Package ppiData version 0.1.10 Index]