| col_by_value | col_by_value |
| download_KEGGfile | download_KEGGfile |
| find_enriched_pathway | find_enriched_pathway |
| parse_XMLfile | parse_XMLfile |
| pho_sites_count | number of phosphorylation sites quantified for each gene |
| plot_pathway | plot_pathway |
| plot_profile | plot_profile |
| pro_pho_expr | expression profiles in proteome and phosphoproteome |