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Direction analysis for pathways and kinases

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Description

`directPA' is a package designed to identify combinatorial effects of multiple treatments and/or perturbations on pathways and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics data.

Download and install

The relsease version can be downloaded from CRAN link;

Install the release version from CRAN with install.packages("directPA")

Examples

I. for kinase anlaysis on a phosphoproteomics dataset (Humphrey et al. Cell Metab., 2013)

# load the phosphoproteomics dataset
data(HEK)

# load the kinase-substrate annoations
data(PhosphoSite)

# direction pathway analysis in 2-dimensional space. Implemented as rotating by degree 
# (1) test combined effect of Torin1 and Rapamycin vs insul both on "down-regulation"
# (180 degree to original direction)
kPA <- kinasePA(Tc=HEK, direction=pi, annotation=PhosphoSite.mouse)
kPA$kinase[order(unlist(kPA$kinase[,1])),][1:20,]
# rank substrates on the direciton of interest
sort(kPA$substrate.pvalues)[1:20]

# (2) test combined effect of Torin1 and Rapamycin vs insul on "no change and down-regulation"
# (135 degree to the original direction) 
kPA <- kinasePA(Tc=HEK, direction=pi*3/4, annotation=PhosphoSite.mouse)
kPA$kinase[order(unlist(kPA$kinase[,1])),][1:20,]

# (3) test combined effect of Torin1 and Rapamycin vs insul on "down-regulation and no change"
# (225 degree to the original direction) 
kPA <- kinasePA(Tc=HEK, direction=pi*5/4, annotation=PhosphoSite.mouse)
kPA$kinase[order(unlist(kPA$kinase[,1])),][1:20,]

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Version

Install

install.packages('directPA')

Monthly Downloads

312

Version

1.5.1

License

GPL-3

Maintainer

Last Published

November 16th, 2023

Functions in directPA (1.5.1)

geneStats

Molecule Level Statistics
directPA

Direction Analysis for Pathways
HEK

Phosphoproteomics of HEK-293E
PhosphoELM.human

PhosphoELM annotations for human
directExplorer2d

Batch Direction Analysis in 2-dimentional space
directPA-package

Direction Pathway Analysis Package
Pathways.reactome

Reactome pathway annotations
PhosphoELM.mouse

PhosphoELM annotations for mouse
PhosphoSite.mouse

PhosphoSitePlus annotations for mouse
PhosphoSite.human

PhosphoSitePlus annotations for human
Pathways.KEGG

KEGG pathway annotations
perturbPlot2d

Perturbation Plot
PM

Plasma Membrame Protoemics Data
pathwayStats

Pathway Level Statistics
perturbPlot3d

Perturbation Plot 3D
kinasePA

Direction Analysis for Kinases
rotate2d

Polar Coordinates Rotation
rotate3d

Spherical Coordinates Rotation