PX: PX dataset for KSEA calculations

In KSEAapp: Kinase-Substrate Enrichment Analysis

Description

A sample PX dataset of the experimental phosphoproteomics input

Usage

data(PX)

Format

the experimental data file must be 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

References

unpublished data

KSEAapp documentation built on May 2, 2019, 3:28 p.m.