SpongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

ABSTRACT:

Motivation

Cancer is one of the leading causes of death worldwide. Despite significant improvements in prevention and treatment, mortality remains high for many cancer types. Hence, innovative methods that use molecular data to stratify patients and identify biomarkers are needed. Promising biomarkers can also be inferred from competing endogenous RNA (ceRNA) networks that capture the gene-miRNA gene regulatory landscape. Thus far, the role of these biomarkers could only be studied globally but not in a sample-specific manner. To mitigate this, we introduce spongEffects, a novel method that infers subnetworks (or modules) from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity.

Results

We show how spongEffects can be used fo

SUBMITTER: Boniolo F 

PROVIDER: S-EPMC10220456 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature