ASEB (version 1.16.0)

asebSites: prediction of lysine sites that can be acetylated

Description

This function is used to predict lysine sites that can be acetylated by a specific KAT-family.

Usage

asebSites(backgroundSites, prodefinedSites, testSites, outputFile=NULL, permutationTimes=10000)
## S3 method for class 'character,character,character':
asebSites(backgroundSites, prodefinedSites, testSites, outputFile=NULL, permutationTimes=10000)
## S3 method for class 'SequenceInfo,SequenceInfo,SequenceInfo':
asebSites(backgroundSites, prodefinedSites, testSites, outputFile=NULL, permutationTimes=10000)

Arguments

backgroundSites
SequenceInfo object or file name (character(1)) for background peptides set.
prodefinedSites
SequenceInfo object or file name (character(1)) for KAT special peptides set.
testSites
SequenceInfo object or file name (character(1)) for query peptides set.
outputFile
file name for output (character(1)).
permutationTimes
permutation times (integer(1)), default and recommended: 10000.

Value

  • The output file contains enrichment scores and P-values for each query site. The asebSites,SequenceInfo,SequenceInfo,SequenceInfo-method also returns a list contains two data.frame objects: results and curveInfo.
  • resultscontains enrichment scores and P-values for each query site.
  • curveInfocontains information for enrichment score curves.

Details

This function is used to predict lysine sites that can be acetylated by a specific KAT-family. It will give an enrichment score and a P-value for each query lysine site. The whole process is similar with the GSEA method (permuting gene sets). Please see the references for details. The first three arguments of method asebSites can be SequenceInfo objects or file names. If these arguments are SequenceInfo objects, this method returns a list to the users besides an output file. Otherwise, this method processes the FASTA format files directly and outputs all results to a file. In this case, this method can process huge number of sites each time without loading any sequences to R workspace.

References

Subramanian, A. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A, 102, 15545-15550. Mootha, V.K. et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet, 34, 267-273. Guttman, M. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.

Li, T.T. et al. Characterization and prediction of lysine (K)-acetyl-transferase (KAT) specific acetylation sites. Mol Cell Proteomics, in press.

See Also

SequenceInfo, readSequence, asebProteins, drawStat, drawEScurve.

Examples

Run this code
backgroundSites <- readSequence(system.file("extdata", "background_sites.fa", package="ASEB")) 
    prodefinedSites <- readSequence(system.file("extdata", "predefined_sites.fa", package="ASEB"))
    testSites <- readSequence(system.file("extdata", "sites_to_test.fa", package="ASEB"))
    resultList <- asebSites(backgroundSites, prodefinedSites, testSites, permutationTimes=100)
    resultList$results[1:2,]

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