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PTM-POSE

Overview:

  • Overview
  • Dependencies
  • PTM-POSE Reference

Instructions:

  • Installation
  • Running PTM-POSE
  • Filtering PTMs and Events
  • Annotating PTMs with Functional Information

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
      • Identify kinases with enriched substrates in differentially included exons, using an adapted version of KSTAR
      • Protein interactions network
    • Analyzing altered flanking sequences
      • Kinase affinity due to PTM flanking sequence alterations
      • Inspect difference of flanking sequence due to splice event
      • Identify altered SH2 domain motifs
      • Probing where and how PTM flanking sequences are altered

Troubleshooting

  • Frequently Asked Questions

Python Module Index

p
 
p
- ptm_pose
    ptm_pose.analyze.annotations
    ptm_pose.analyze.enzyme
    ptm_pose.analyze.filter
    ptm_pose.analyze.flanking_sequences
    ptm_pose.analyze.interactions
    ptm_pose.analyze.summarize
    ptm_pose.annotate
    ptm_pose.flanking_sequences
    ptm_pose.pose_config
    ptm_pose.project

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