apComplex (version 2.38.0)

TAP complexes: TAP data complex estimates

Description

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

Usage

data(MBMEcTAP)
data(SBMHcTAP)
data(UnRBBcTAP)

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).

Details

These are the results from an analysis of the TAP data (Gavin et al., 2002) 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 .995, and Beta=-0.2 for externally derived similarity measure based on Gene Ontology cellular component annotation (see Scholtens and Gentleman (2004)).

MBMEcTAP contains 260 multi-bait-multi-edge complex estimates. SBMHcTAP contains 325 single-bait-multi-hit complex estimates. UnRBBcTAP contains 123 unreciprocated bait-bait complex estimates. These data are also available at http://www.bioconductor.org/Docs/Papers/2003/apComplex.

References

Gavin, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).

See Also

TAP, TAPgraph, yTAP, findComplexes

Examples

data(MBMEcTAP)
MBMEcTAP[1:10,1:3]
which(MBMEcTAP[,"MBME1"]==1)