- Phosphorylation Data Analysis 77
Figure 1. An example layout of quantitative phosphosite data for use in DynaPho.software and prepare in the form of tab-delimited text files (Fig. 1). The
required columns of input data for DynaPho include:
- UniProt ID. If a phosphorylated site maps to multiple proteins, the IDs
are delimited by “;”. - Phosphorylation position on protein. For multiple hits, the values are
delimited by “;”. - Phosphorylation residue (S, T, or Y).
- n-mer sequence window around the phosphorylated residues (5≤n≤15,
wherenis odd number). Empty positions for N- or C-terminal peptides
have to be filled up manually with an underline character (“−”) for each
gap. - Time-series quantitative values (Ratio). Base-2 logarithmic transforma-
tion of ratio value is recommended. The number of columns is based on
your phosphoproteomics data.
Procedure
Submission of user’s phosphoproteomic data
- Start the web browser and load http://dynapho.jhlab.tw/.
- Click on “New Job” on the header.
- Choose the file and click on “Submit”.
- In “Edit Attributes” page, users can modify the column names and check
whether the variable mapping is correct (Fig. 2). Once the settings are
correct, click “Next” to start the data process.