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

ORF1
  The ORF for gene 1
GENE1
  The symbol for gene 1
ORF2
  The ORF for gene 2
GENE2
  The symbol for gene 2
DESCR
  A description of one, or both genes
EVI
  An evidence code.

### 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]