KSEA.Complete: The Complete KSEA App Analysis
In KSEAapp: Kinase-Substrate Enrichment Analysis

Description Usage Arguments Value References Examples

Takes a formatted phoshoproteomics data input and performs KSEA calculations to infer relative kinase activities

1	KSEA.Complete(KSData, PX, NetworKIN, NetworKIN.cutoff, m.cutoff, p.cutoff)

`KSData`	the Kinase-Substrate dataset uploaded from the file prefaced with "PSP&NetworKIN_" available from github.com/casecpb/KSEA/
`PX`	the experimental data file formatted exactly as described below; must have 6 columns in the exact order: Protein, Gene, Peptide, Residue.Both, p, FC; cannot have NA values, or else the entire peptide row is deleted; Description of each column in PX: "Protein" the Uniprot ID for the parent protein "Gene" the HUGO gene name for the parent protein "Peptide" the peptide sequence "Residue.Both" all phosphosites from that peptide, separated by semicolons if applicable; must be formatted as the single amino acid abbrev. with the residue position (e.g. S102) "p" the p-value of that peptide (if none calculated, please write "NULL", cannot be NA) "FC" the fold change (not log-transformed); usually the control sample is the denominator
`NetworKIN`	a binary input of TRUE or FALSE, indicating whether or not to include NetworKIN predictions; NetworKIN = TRUE means inclusion of NetworKIN predictions
`NetworKIN.cutoff`	a numeric value between 1 and infinity setting the minimum NetworKIN score (can be left out if NetworKIN = FALSE)
`m.cutoff`	a numeric value between 0 and infinity indicating the min. # of substrates a kinase must have to be included in the bar plot output
`p.cutoff`	a numeric value between 0 and 1 indicating the p-value cutoff for indicating significant kinases in the bar plot

creates the following outputs that are deposited into your working directory: a bar plot highlighting key kinase results, a .csv file of all KSEA kinase scores, and a .csv file listing all kinase-substrate relationships used for the calculations

Casado et al. (2013) Sci Signal. 6(268):rs6

Hornbeck et al. (2015) Nucleic Acids Res. 43:D512-20

Horn et al. (2014) Nature Methods 11(6):603-4

1 2	KSEA.Complete(KSData, PX, NetworKIN=TRUE, NetworKIN.cutoff=5, m.cutoff=5, p.cutoff=0.01) KSEA.Complete(KSData, PX, NetworKIN=FALSE, m.cutoff=2, p.cutoff=0.05)