DDK-Linker

DDK-Linker connects lists of differentially expressed genes or proteins (GOIs) to known disease genes via protein-protein interaction (PPI) networks to discover disease-associated signals in high-throughput omics data.

Key Features:

• Network-Based Strategy: Leverages the protein-protein interaction (PPI) network to establish biologically plausible linkages between GOIs and established disease-related genes.
• Reconstruction of Gene Distances: Reconstructs gene distances within the PPI network using six network methods: random walk with restart, Deepwalk, Node2Vec, LINE, HOPE, and Laplacian.
• Integration of Bioinformatics Annotations: Associates candidate disease signals with comprehensive bioinformatics annotations to enrich biological interpretation.

Scientific Applications:

• Disease signal discovery in omics: Identifies disease-associated signals across genomics, transcriptomics, and proteomics datasets.
• Drug target and disease-gene exploration: Supports identification of potential disease genes and drug targets by linking GOIs to known disease knowledge.

Methodology:

Uses the PPI network to connect GOIs and known disease genes and reconstructs gene distances with random walk with restart, Deepwalk, Node2Vec, LINE, HOPE, and Laplacian, then annotates candidate signals with bioinformatics annotations.