CompleXChange

CompleXChange infers protein complex abundances and detects deregulated protein complexes by integrating predicted or manually assigned complexes with transcriptomic and proteomic data at whole-genome scale.

Key Features:

• Whole-Genome Scale Application: Analyzes complexomes at whole-genome scale by integrating input from transcriptomic and proteomic studies.
• Inferred Complex Abundance Estimation: Employs an advanced algorithm to estimate protein complex abundances with superior accuracy compared to linear programming on simulated datasets while remaining computationally efficient.
• Robustness and Accuracy: Reduces false-positive detections to reliably identify deregulated complexomes that are not fully explained by differential analysis at the individual protein-coding gene level.
• Validation in Human Samples: Validated on transcription factor complexes in human monocyte and lymphoblastoid samples.
• Significant Information Content: Identifies deregulated complexes that reveal previously underutilized information about biological processes and disease mechanisms.

Scientific Applications:

• Complex assembly and regulation studies: Investigates dynamic assembly and regulation of protein complexes across conditions using integrated complexome data.
• Multi-omics and systems biology: Provides insights into cellular functions and regulatory mechanisms not apparent from individual protein analyses, supporting research in systems biology, genomics, and proteomics.

Methodology:

Integration of predicted or manually assigned complexes with inferred complex abundances using an advanced abundance-estimation algorithm, with performance benchmarked against linear programming on simulated datasets.