PTR

PTR identifies post-transcriptional regulatory mechanisms by integrative proteogenomic analysis of transcriptomic and proteomic abundances using scatterplot diagnostics (scagnostics) to detect non-linear gene–protein relationships.

Key Features:

• Integrative Proteogenomic Analysis: Combines transcriptomic and proteomic data to analyze transcript and protein abundances in a unified proteogenomic framework.
• Scatterplot Diagnostics (Scagnostics): Applies scatterplot diagnostics (scagnostics) to characterize diverse geometric patterns of gene–protein relationships derived from transcript and protein abundances.
• Clustering on Geometric Features: Clusters genes based on geometric scagnostic features of their scatterplots to group gene–protein relationships according to PTR dispositions.
• Pattern-Specific Analyses: Provides downstream analysis approaches including mixture modeling and mapping of miRNA post-transcriptional effects to interrogate specific PTR patterns.
• Validation on Synthetic Data: Evaluates method robustness and applicability through comprehensive tests on synthetic datasets.

Scientific Applications:

• Cancer Research: Reveals proteogenomic trends and provides evidence for cancer-specific post-transcriptional regulatory mechanisms, including impacts related to biological functionality and degradation types.
• miRNA Targeting: Maps miRNA effects on post-transcriptional regulation to clarify miRNA roles in gene expression modulation.
• Regulatory Mechanism Discovery: Categorizes post-transcriptional regulatory mechanisms to facilitate discovery of novel regulatory pathways and their implications in disease contexts.

Methodology:

Represent gene–protein relationships as scatterplots, compute geometric scagnostic features, cluster genes on those scagnostic features, perform downstream mixture modeling and mapping of miRNA post-transcriptional effects, and validate the approach on synthetic datasets.