| Title: | Yeast Gold Standard Data |
|---|---|
| Description: | A collection of so-called gold (and other) standard data sets |
| Authors: | R. Gentleman |
| Maintainer: | R. Gentleman <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 0.50.0 |
| Built: | 2026-10-10 11:01:10 UTC |
| Source: | https://github.com/bioc/yeastGSData |
This data consists of the 7739 binary interactions with computed Bayes factor of less than -3. This dataset was created 16 June 2009.
data(BayesFactorNGS)data(BayesFactorNGS)
A data frame with observations on the following 5 variables.
Orf1The ORF for gene 1
Orf2The ORF for gene 2
TestedThe number of times the interaction was tested
ObservedThe number of times the interaction was found
log_BFThe log of the resulting Bayes factor
None.
data(BayesFactorNGS)data(BayesFactorNGS)
This data consists of the 10200 binary interactions with computed Bayes factor of greater than 3. This dataset was created 16 June 2009.
data(BayesFactorPGS)data(BayesFactorPGS)
A data frame with observations on the following 5 variables.
Orf1The ORF for gene 1
Orf2The ORF for gene 2
TestedThe number of times the interaction was tested
ObservedThe number of times the interaction was found
log_BFThe log of the resulting Bayes factor
None.
data(BayesFactorPGS)data(BayesFactorPGS)
This data consists of the 1318 binary interactions Yu et al reported as their binary gold standard data set.
data(BinaryGS)data(BinaryGS)
A data frame with 1318 observations on the following 2 variables.
ORF1The ORF for gene 1
ORF2The ORF for gene 2
None.
The data were downloaded from http://interactome.dfci.harvard.edu/S_cerevisiae on Nov 21, 2008.
H. Yu et al, High Quality Binary Protein Interaction Map of the Yeast Interactome Network, Science 322, 104, 2008.
data(BinaryGS)data(BinaryGS)
The MIPS gold standard protein complex data set downloaded from the Gerstein Lab web site.
data(MIPSGS)data(MIPSGS)
A data frame with 8617 observations on the following 5 variables.
ORF1The ORF for one gene
ORF2The ORF for the second gene
CIDThe MIPS protein complex ID
NAMEThe name of the complex.
NUMBERThe number of proteins in the complex.
The data are essentially multiprotein complexes, curated from MIPS data,
see also the data set in Mpact, which is related.
The data are all pairwise members of each complex.
Yu et al. state “ To compile a reference data set with the lowest false-positive rate, we consider two proteins as interaction part- ners if and only if they are in the same complex of the highest level in the catalog. ”
http://interolog.gersteinlab.org
Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs, H. Yu et al, Genome Research, 1107-1118, 2004.
data(MIPSGS)data(MIPSGS)
The data are protein interactions, downloaded from MPACT. They are stored in a large character matrix, with seven columns, describing the interactions.
data(Mpact)data(Mpact)
The data are stored as a matrix, with columns
ORF1The ORF for gene 1
GENE1The symbol for gene 1
ORF2The ORF for gene 2
GENE2The symbol for gene 2
DESCRA description of one, or both genes
EVIAn evidence code.
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,]data(Mpact) Mpact[1:3,]
The data in Mpact are interaction data from MIPS. Each interaction
has one or more evidence code, that is intended to document the basis
on which an interaction is presumed.
data(MpactEvidenceCodes)data(MpactEvidenceCodes)
A character vector of the descriptions, with names given by the evidence codes.
There is a nesting in the evidence codes that is not directly reflected in this data. The first three names are 901, 901.01 and 901.01.01, so the first is a top level term, the second is nested under it, and the third under the second.
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(MpactEvidenceCodes) MpactEvidenceCodes[1:3]data(MpactEvidenceCodes) MpactEvidenceCodes[1:3]
These data were supplied as supplementary material, for the paper below, as a data set for negative interactions.
data(NEGGS)data(NEGGS)
A data frame with 2708746 observations on the following 4 variables.
ORF1The ORF of one interactor.
ORF2The ORF of the second interactor.
LOC1A description of where the first interactor is (typically) located in the cell.
LOC2A description of where the first interactor is (typically) located in the cell.
The data are potentially problematic, since not being in the same cellular component does not mean that two proteins will not interact in some particular assay.
Only a very broad grouping of location is given, and one may want to refer to a more recent and potentially more authoratative source.
http://interolog.gersteinlab.org
Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs, H. Yu et al, Genome Research, 1107-1118, 2004.
data(NEGGS) table(NEGGS$LOC1) table(NEGGS$LOC2)data(NEGGS) table(NEGGS$LOC1) table(NEGGS$LOC2)
While Yu et al. call this a platinum standard data set, it is really a gold standard data set for binary physical interactions.
data(POSPS)data(POSPS)
A data frame with 1867 observations on the following 2 variables.
ORF1a character vector
ORF2a character vector
These data, reported in the paper below, are intended to represent well
established binary physical interactions between proteins. This contrasts
with the gold standard MIPSGS which describes
multi-protein complexes.
Ye et al, describe the construction as follows: “ Briefly, the data set contains physical interactions from complex protein structures in the Protein Data Bank (Westbrook et al. 2003), verified interactions from small-scale experiments (Mewes et al. 2000; Xenarios et al. 2002; Bader et al. 2003), and protein pairs from small MIPS catalog complexes (4 or fewer subunits).”
Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs, H. Yu et al, Genome Research, 1107-1118, 2004.
data(POSPS)data(POSPS)
These data consist of the 188 binary interactions that Yu et al curated and referred to as the positive reference set.
data(PRS)data(PRS)
A data frame with 188 observations on the following 2 variables.
ORF1The ORF for gene 1.
ORF2The ORF for gene 2.
None.
The data were downloaded from http://interactome.dfci.harvard.edu/S_cerevisiae on Nov 21, 2008.
H. Yu et al, High Quality Binary Protein Interaction Map of the Yeast Interactome Network, Science 322, 104, 2008.
data(PRS) ## maybe str(PRS) ; plot(PRS) ...data(PRS) ## maybe str(PRS) ; plot(PRS) ...