magrene

magrene identifies and analyzes graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs, and enables motif enrichment testing and interaction similarity calculation.

Key Features:

• Motif Identification: Identifies lambda, V, PPI V, delta, and bifan motifs in gene regulatory networks.
• Motif Enrichment Testing: Compares motif frequencies to a null distribution generated from degree-preserving simulated GRNs.
• Duplication Analysis: Analyzes motif frequencies in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks.
• Interaction Similarity: Calculates interaction similarity for gene pairs based on the Sorensen-Dice similarity index.

Scientific Applications:

• Gene Regulatory Network Analysis: Identifies and characterizes graph motifs in duplicated and non-duplicated GRNs.
• Duplication Impact Studies: Investigates how small-scale and whole-genome duplications affect network structure through motif frequency analysis.
• Motif Enrichment Analysis: Determines whether observed motif frequencies are statistically significant compared to randomized null models.
• Gene Pair Similarity Assessment: Quantifies interaction similarity between gene pairs using the Sorensen-Dice similarity index.

Methodology:

motif frequencies are compared to a null distribution generated from degree-preserving simulated GRNs; interaction similarity is calculated using the Sorensen-Dice similarity index.