PTMsToPathways Data

This repsitory contains data to be used in the vignettes in the PTMsToPathways R package. All data is also accessible via the PTMsToPathwaysData ExperimentHub package on Bioconductor. Full descriptions, including scripts to regenerate rda files and vignettes demonstrating use of the data, are available in the PTMsToPathwaysData package. Below, we give short descriptions of the data, organized by which PTMsToPathways vignette uses them. Getting started with PTMsToPathways vignette: AlldataPTMs.txt is a table of PTM intensities for over 9,000 PTMs and 69 experimental conditions. ex_full_ptm_table.rda is a dataframe of the above file. Raw data processing vignette: phospho_cleaned_mapped.txt is the output of a mass spectrometry experiment measuring PTM intensities. newphos.rda is a dataframe of the above file. Cytoscape graphing vignette: FunctionKey.txt is a mapping from genes to their functions. function_key.rda is a dataframe of the above file. BRCA Networks vignette: bioplanet_pathway_June2025.csv is a list of pathways from BioPlanet. bioplanet_pathways.rda is a dataframe of the above. PhosphoDiscoData_mmc9.txt is Supplementary Table 2 from Schraink et al. 2023 brca_clusterlist_data.rda is the PTM cluster data created by PTMsToPathways on the Schraink et al. data. BRCA_stringdb.edges.rda is an intermediate output of the PTMsToPathways functions. BRCA_genemania.edges.rda is an intermediate output of the PTMsToPathways functions. brca_CCCN_data.rda is the Co-Cluster Correlation Network created by PTMsToPathways on the Schraink et al. data. BRCA_PCN.data.rda is the Pathway Crosstalk Network created by PTMsToPathways on the Schraink et al. data.