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 [email protected]
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