Characterizing alternative splicing effects on protein interaction networks with LINDA.

ABSTRACT:

Motivation

Alternative RNA splicing plays a crucial role in defining protein function. However, despite its relevance, there is a lack of tools that characterize effects of splicing on protein interaction networks in a mechanistic manner (i.e. presence or absence of protein-protein interactions due to RNA splicing). To fill this gap, we present Linear Integer programming for Network reconstruction using transcriptomics and Differential splicing data Analysis (LINDA) as a method that integrates resources of protein-protein and domain-domain interactions, transcription factor targets, and differential splicing/transcript analysis to infer splicing-dependent effects on cellular pathways and regulatory networks.

Results

We have applied LINDA to a panel of 54 shRNA depletion expe

SUBMITTER: Gjerga E 

PROVIDER: S-EPMC10311343 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature