RNAsense

RNAsense compares RNA-seq time curves in two experimental conditions to identify dynamic transcript expression profiles and correlate them with differential expression patterns.

Key Features:

• Expression Profile Building: Constructs expression profiles for each transcript in one condition and tests whether transcript abundance grows or decays significantly.
• Time Profile Grouping: Sorts dynamic transcripts into non-overlapping groups (time profiles) by the time point of switch up or down.
• Differential Expression Analysis: Outputs groups of differentially expressed transcripts that are up- or downregulated in the mutant compared to the wild-type at each time point.
• Correlation Analysis: Calculates correlations between switch up-/switch down- time profile groups and differentially expressed transcript groups using Fisher's exact test.
• Visualization: Displays correlation analysis results as a two-dimensional color plot with time profiles on the y-axis and differential expression groups on the x-axis.

Scientific Applications:

• Time-Resolved RNA-Seq Analysis: Analyzes RNA-seq time curves from wild-type and mutant experimental conditions to study temporal gene expression dynamics.
• Transcript Dynamics Classification: Identifies and classifies transcripts with significant growth or decay patterns over time.
• Genotype-Expression Correlation: Correlates temporal expression switches with genotype-dependent differential expression to facilitate biological interpretation.

Methodology:

RNAsense operates in three steps: Step 1 builds expression profiles for each transcript in one condition and tests for significant growth or decay, then sorts dynamic transcripts into non-overlapping time profile groups by switch up or down time point. Step 2 identifies differentially expressed transcripts up- or downregulated in the mutant compared to wild-type at each time point. Step 3 calculates correlations between Step 1 time profile groups and Step 2 differential expression groups using Fisher's exact test.