PTM-POSE

Overview:

• Overview
• Dependencies
• Optional Dependencies
• PTM-POSE Reference
  • Configuration
    • download_translator()
  • PTM Projection
    • find_ptms_in_region()
    • project_ptms_onto_MATS()
    • project_ptms_onto_SpliceSeq()
    • project_ptms_onto_splice_events()
  • Flanking Sequences
    • get_flanking_changes()
    • get_flanking_changes_from_rMATS()
    • get_flanking_changes_from_splice_data()
    • get_flanking_changes_from_splicegraph()
  • Annotating PTMs
    • add_ELM_interactions()
    • add_ELM_matched_motifs()
    • add_custom_annotation()
    • add_omnipath_data()
    • annotate_ptms()
    • append_from_gmt()
    • check_file()
    • check_gmt_file()
    • combine_enzyme_data()
    • combine_interaction_data()
    • construct_DEPOD_gmt_file()
    • construct_PTMInt_gmt_file()
    • construct_PTMcode_interprotein_gmt_file()
    • construct_PTMsigDB_gmt_files()
    • construct_PhosphoSitePlus_gmt_files()
    • construct_RegPhos_gmt_file()
    • construct_annotation_dict_from_df()
    • construct_annotation_dict_from_gmt()
    • construct_combined_enzyme_gmt_df()
    • construct_combined_interactions_gmt_df()
    • construct_custom_gmt_file()
    • construct_gmt_df()
    • construct_omnipath_gmt_file()
    • convert_PSP_label_to_UniProt()
    • extract_ids_PTMcode()
    • extract_interaction_details()
    • extract_positions_from_DEPOD()
    • get_available_gmt_annotations()
    • load_gmt_file()
    • process_database_annotations()
    • simplify_annotation()
    • unify_interaction_data()
  • Analyze Modules
    • Summaries
      • combine_outputs()
      • get_modification_class_data()
      • get_modification_counts()
      • plot_modification_breakdown()
    • Filtering PTMs and Events
      • assess_filter_range()
      • plot_filter_impact()
    • Annotations
      • annotation_enrichment()
      • draw_pie()
      • gene_set_enrichment()
      • get_available_annotations()
      • get_background_annotation_counts()
      • get_enrichment_inputs()
      • get_ptm_annotations()
      • plot_EnrichR_pies()
      • plot_annotation_counts()
      • plot_available_annotations()
    • Protein Interactions
      • get_edge_colors()
      • get_interaction_stats()
      • plot_interaction_network()
      • plot_network_centrality()
      • protein_interactions
    • Enzyme Regulation
      • compare_KL_for_sequence()
      • get_all_KL_scores()
    • Flanking Sequences
      • compare_flanking_sequences()
      • compare_inclusion_motifs()
      • findAlteredPositions()
      • find_motifs()
      • getSequenceIdentity()
      • identify_change_to_specific_motif()
      • plot_alterations_matrix()
      • plot_location_of_altered_flanking_residues()
      • plot_sequence_differences()

Instructions:

• Installation
  • Installation
• Running PTM-POSE
  • Formatting Data
  • Identifying differentially included PTMs
  • Altered Flanking Sequences
  • Using PTM-POSE with MATS or SpliceSeq datasets
    • MATS datasets
    • SpliceSeq datasets
• Filtering PTMs and Events
  • Types of Available Filters
  • How to Filter PTMs and Events
    • Filtering PTMs during Projection
    • Filtering PTMs during analysis
  • Why Filter?
  • Impact of Filtering PTMs by evidence
• Annotating PTMs with Functional Information
  • Annotating PTMs with pre-installed annotation files
  • Updating annotation files
  • Creating Custom Annotation files
  • Future Directions

Example Vignettes

• Examples
  • ESRP1 Knockdown (MATS output)
  • ESRP1 Expression in Prostate Cancer (TCGASpliceSeq output)

Analysis Gallery

• Gallery
  • General Overview of Spliced PTMs
  • Functional Impact of Spliced PTMs
  • Impact on protein interaction and regulatory networks
  • Analyzing altered flanking sequences

Troubleshooting

• Frequently Asked Questions
  • Data sources
  • Data Preparation
  • Interpreting Results

Indices and tables

• Index

• Module Index

• Search Page