A pipeline to gather snoRNA and RBP interactions to perform a sno-RBP interaction network analysis.

Dependencies:

• snakemake
• bedtools=2.29.0
• pandas

Author: Kristina Sungeun Song kristina.song@usherbrooke.ca

Inputs:

• RBP data downloaded from ENCODE
  • Target category: select 'RNA binding protein'
• snoGloBe predictions against all protein coding biotypes
• snoDB: all snoRNAs that have protein coding host genes
• HTRRI
• list of snoRNAs (Ensembl_id, name, type)
• list of RBPs (protein_id, name, type)

Types of snoRNA-RBP Interactions:

• Overlap of target sites:
  • snoRNA-snoRNA
  • RBP-RBP
  • snoRNA-RBP
• Direct binding interactions:
  • snoRNA binds to RBP mRNA transcript
  • RBP binds to snoRNA transcript
• Interactions from external database:
  • STRING RBP-RBP binding interactions
  • High-throughput RNA-RNA interactions: PARIS, SPLASH, LIGR-seq
  • snoRNA embedded in host genes that encode for RBP