Mpact {yeastGSData}R Documentation

Protein Interaction Data from Mpact

Description

The data are protein interactions, downloaded from MPACT. They are stored in a large character matrix, with seven columns, describing the interactions.

Usage

data(Mpact)

Format

The data are stored as a matrix, with columns

Details

It is unlikely that the variables GENE1 and GENE2 can be relied on, as names change, so ORF1 and ORF2 should be preferred, and even these should be compared to current databases to see if they have been supplanted.

The DESCR field is incomplete, and seems to be inconsistent. It would probably better to rely on the the ORFs to obtain documentation on the ORFs from other sources.

The EVI variable, gives one, or more evidence codes, separate by commas ,. The evidence codes are further detailed in the MpactEvidenceCodes data object. Evidence codes can be helpful in filtering out interactions that might give rise to circularity in an analysis. By that we mean, that if you are analyzing data that comes from one of the experiments that was used to establish this gold standard data set, it might be best to filter those interactions out. You should be careful to only filter them, if their only evidence is from the experiment you are analyzing (if there is other evidence for the interaction it should be retained).

Source

The data were downloaded from ftp://ftpmips.gsf.de/yeast/PPI/.

References

Guldener U, Munsterkotter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stumpflen V(2006). MPact: the MIPS protein interaction resource on yeast. Nucl. Acids Res. 2006 34: D436-D441 PMID: 16381906

See Also

MpactEvidenceCodes

Examples

data(Mpact)
Mpact[1:3,]

[Package yeastGSData version 0.1.2 Index]