fastLiquidAssociation

fastLiquidAssociation performs genome-wide liquid association (LA) analysis to identify gene triplets where the coexpression of two genes depends on the expression level of a third controller gene.

Key Features:

• Efficient Screening Algorithm: Implements a screening method that reduces the number of gene triplets requiring examination while achieving over 99.8% agreement with exhaustive search and reducing computational run time by 81–93% on a Saccharomyces cerevisiae test subset.
• Genome-wide Application: Enables LA estimation across entire genomes to address scalability and resource limitations of traditional LA methods.
• Significance Analysis Integration: Provides code for conducting subsequent significance analyses on triplets with large LA values.
• Exploratory Gene Set Enrichment Analysis: Facilitates exploratory analyses to associate controller genes in significant triplets with biological processes such as energy regulation, transportation, and sporulation in yeast datasets.

Scientific Applications:

• Gene regulatory network discovery: Detects controller-dependent coexpression patterns to reveal regulatory relationships and pathways among genes.
• Empirical application in yeast: Applied to a Saccharomyces cerevisiae cell-cycle dataset comprising 6,178 genes to identify triplet combinations with significantly large LA values.
• Cross-organism applicability: Applicable to genome-wide LA analyses in organisms beyond yeast to investigate dynamic gene interactions.

Methodology:

Uses a fast screening algorithm for genome-wide LA estimation, followed by significance analyses of identified triplets and exploratory gene set enrichment analysis on controller genes.