Mpact {yeastGSData} | R Documentation |
The data are protein interactions, downloaded from MPACT. They are stored in a large character matrix, with seven columns, describing the interactions.
data(Mpact)
The data are stored as a matrix, with columns
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).
The data were downloaded from ftp://ftpmips.gsf.de/yeast/PPI/.
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
data(Mpact) Mpact[1:3,]