HMSPCI complexes {apComplex}R Documentation

HMSPCI data complex estimates

Description

Affiliation matrices with rows corresponding to proteins and columns corresponding to complexes.

Usage

data(MBMEcHMSPCI)
data(SBMHcHMSPCI)
data(UnRBBcHMSPCI)

Details

These are the results from an analysis of the HMS-PCI data (Ho et al., 2002) described by Scholtens and Gentleman (2004) and Scholtens, Vidal, and Gentleman (submitted). These estimates were constructed using findComplexes with a sensitivity parameter of .75, specificity of .99, and Beta=-0.2 for externally derived similarity measure based on Gene Ontology cellular component annotation (see Scholtens and Gentleman (2004)).

MBMEcHMSPCI contains 242 multi-bait-multi-edge complex estimates. SBMHcHMSPCI contains 437 single-bait-multi-hit complex estimates. UnRBBcHMSPCI contains 329 unreciprocated bait-bait complex estimates. These data are also available at http://www.bioconductor.org/Docs/Papers/2003/apComplex.

Source

Scholtens D and Gentleman R. Making sense of high-throughput protein-protein interaction data. Statistical Applications in Genetics and Molecular Biology 3, Article 39 (2004).

Scholtens D, Vidal M, and Gentleman R. Local modeling of global interactome networks. Bioinformatics 21, 3548-3557 (2005).

References

Ho, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).

See Also

HMSPCI,HMSPCIgraph,\code{findComplexes}

Examples

data(MBMEcHMSPCI)
MBMEcHMSPCI[1:4,1:4]
which(MBMEcHMSPCI[,"MBME1"]==1)


[Package apComplex version 2.2.0 Index]