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PTM-POSE

Overview:

  • What is PTM-POSE?
  • Dependencies
  • Installation
  • PTM-POSE Reference

Running PTM-POSE

  • Projecting PTMs onto Splice Events
  • Annotating PTMs with Functional Information
  • Analyzing PTM Impacts

Example Vignettes

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

Analysis Gallery

  • Gallery
    • General Overview of Spliced PTMs
      • Inspecting types of PTMs impacted by splicing
      • Inspecting number of PTMs with annotation information available
      • Impact of filtering PTMs
    • Functional Impact of Spliced PTMs
      • Identifying available PTM-specific annotation information
      • Identify enriched gene sets associated with differentially spliced PTMs
      • Assessing enriched PTM functions
    • Impact on protein interaction and regulatory networks
      • Kinase substrate enrichment analysis (KSEA)
      • Protein interactions network
      • Identify kinases with enriched substrates in differentially included exons, using an adapted version of KSTAR
    • Analyzing altered flanking sequences
      • Inspect difference of flanking sequence due to splice event
      • Identify altered SH2 domain motifs
      • Probing where and how PTM flanking sequences are altered
      • Kinase affinity due to PTM flanking sequence alterations

Additional Topics

  • Filtering PTMs and Events
  • Frequently Asked Questions
  • .rst

  • Projecting PTMs onto Splice Events
    • Formatting Data
      • Tools with Built-in Compatibility
      • Other Quantification Tools
    • Running PTM-POSE
      • MATS Datasets
      • SpliceSeq Datasets
      • MAJIQ Datasets (voila tsv files)
      • Other Datasets
    • Downstream Analysis
  • Annotating PTMs with Functional Information
    • Available Annotations
    • Appending Annotations to PTM Dataframes
    • Updating annotation files
    • Creating Custom Annotation files
    • Future Directions
  • Analyzing PTM Impacts

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PTM-POSE Reference

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Projecting PTMs onto Splice Events

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