TAP: Tandem Affinity Purification (TAP) Data from Gavin et al....

In apComplex: Estimate protein complex membership using AP-MS protein data

Description

TAP data published by Gavin, et al. (2002).

Usage

data(TAP)
data(TAPgraph)

Details

TAP is a matrix of the TAP data published by Gavin, et al. (2002). The 455 rows correspond to bait proteins and the 1364 columns correspond to proteins found as hits in the TAP experiment and are named accordingly. The first 455 column names are the same as the 455 row names; bait proteins can also be found as hits by other baits, hence their inclusion as columns in TAP. An entry of "1" in the ith row and jth column of TAP indicates that bait protein i found protein j as a hit. All other entries are "0". There are a total of 3420 "1" entries in the matrix, corresponding to the 3420 comemberships detected in the experiment.

TAPgraph is a graphNEL object in which 1364 nodes represent proteins and 3420 directed edges represent comemberships detected in the purification. Each directed edge originates at the bait and ends at the hit. Each edge in TAPgraph corresponds to an entry of "1" in the TAP matrix.

These data are available in Supplementary Table S1 of Gavin et al. at http://www.nature.com.

Source

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

References

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).

See Also

yTAP,MBMEcTAP,SBMHcTAP,UnRBBcTAP,HMSPCI

Examples

data(TAP)
which(TAP["Abd1",]==1)

data(TAPgraph)
adj(TAPgraph,"Abd1")

Example output

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: RBGL

Rpb2 Spt5 
 926 1049 
$Abd1
[1] "Rpb2" "Spt5"

apComplex documentation built on Nov. 8, 2020, 7:43 p.m.