ProteoMirExpress

ProteoMirExpress integrates proteomic and mRNA expression data to infer miRNA-centered regulatory networks that capture miRNA effects such as translational repression and RNA degradation.

Key Features:

• Integration of Multi-Omics Data: Combines proteomic data with mRNA expression data to reveal regulatory effects observable at the protein level in addition to transcript level.
• Discovery of Diverse miRNA Targets: Identifies targets with suppressed protein expression despite unchanged mRNA levels and targets with decreased mRNA whose corresponding proteins are not significantly altered.
• Comprehensive Network Inference: Constructs miRNA-centered regulatory networks that encompass direct and indirect miRNA effects across integrated datasets.
• Validation and Quality Assessment: Performance has been evaluated using several published datasets to assess the accuracy of inferred regulatory networks.

Scientific Applications:

• Analysis of direct and indirect miRNA effects: Enables identification and characterization of both direct targets and downstream indirect effects of miRNAs on gene expression.
• Investigation of mRNA–protein discordance: Facilitates study of cases where protein-level changes do not parallel mRNA-level changes, implicating translational regulation by miRNAs.
• Identification of novel miRNA targets: Supports discovery of potential miRNA targets that may be missed by mRNA-only analyses.

Methodology:

Integrates proteomic and mRNA expression datasets to infer miRNA-centered regulatory networks and validates inferred networks using published datasets.