HMSPCI: High-Throughput Mass Spectromic Protein Complex...

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

Description

HMS-PCI data published by Ho, et al. (2002).

Usage

data(HMSPCI)
data(HMSPCIgraph)

Details

HMSPCI is a matrix of the HMS-PCI data published by Ho, et al. (2002). The 493 rows correspond to bait proteins and the 1578 columns correspond to proteins found as hits in the HMSPCI experiment and are named accordingly. The first 493 column names are the same as the 493 row names; bait proteins can also be found as hits by other baits, hence their inclusion as columns in HMSPCI. An entry of "1" in the ith row and jth column of HMSPCI indicates that bait protein i found protein j as a hit. All other entries are "0". There are a total of 3687 "1" entries in the matrix, corresponding to the 3687 comemberships detected in the experiment.

HMSPCIgraph is a graphNEL object in which 1578 nodes represent proteins and 3687 directed edges represent comemberships detected in the purification. Each directed edge originates at the bait and ends at the hit. Each edge in HMSPCIgraph corresponds to an entry of "1" in the HMSPCI matrix.

These data are available at http://www.mdsp.com/yeast.

Source

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

MBMEcHMSPCI,SBMHcHMSPCI,UnRBBcHMSPCI,TAP

Examples

data(HMSPCI)
which(HMSPCI["YAL015C",]==1)

data(HMSPCIgraph)
adj(HMSPCIgraph,"YAL015C")

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

YDL029W YJR068W YMR146C YPR110C YDR214W YEL030W YEL060C YMR012W YMR058W YNL037C 
     62     280     367     488     704     759     765    1274    1279    1333 
$YAL015C
 [1] "YDL029W" "YJR068W" "YMR146C" "YPR110C" "YDR214W" "YEL030W" "YEL060C"
 [8] "YMR012W" "YMR058W" "YNL037C"

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