A sample PX dataset of the experimental phosphoproteomics input

datasets

Infers relative kinase activity from phosphoproteomics data
using the method described by Casado et al. (2013) <doi:10.1126/scisignal.2003573>.

Danica Wiredja

KSEAapp

Kinase-Substrate Enrichment Analysis

PX function

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: 
          <ul>
<li>&quot;Protein&quot; the Uniprot ID for the parent protein 
              </li>
<li>&quot;Gene&quot; the HUGO gene name for the parent protein 
              </li>
<li>&quot;Peptide&quot; the peptide sequence
              </li>
<li>&quot;Residue.Both&quot; 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)
              </li>
<li>&quot;p&quot; the p-value of that peptide (if none calculated, please write &quot;NULL&quot;, cannot be NA)
              </li>
<li>&quot;FC&quot; the fold change (not log-transformed); usually the control sample is the denominator
              </li>
</ul>

PX: PX dataset for KSEA calculations

Description

Usage

Arguments

Format

References