TIPS

TIPS infers pathway significance along developmental trajectories from single-cell RNA sequencing (scRNAseq) data by integrating pathway knowledgebases and gene-level signals.

Key Features:

• Pathway Contribution Analysis: Leverages knowledgebases of functional pathways and curated gene lists to identify pathways that significantly influence a specified biological trajectory.
• Gene Identification: Identifies individual genes within those pathways whose expression best reflects changes along the inferred trajectory.
• Temporal Insights: Determines the timing of pathway activity changes across developmental or differentiation trajectories.
• Visualization Suite: Produces visualizations tailored to scRNAseq libraries that represent pathway contributions, gene dynamics, and temporal changes along trajectories.

Scientific Applications:

• Developmental biology: Dissects how specific pathways contribute to cellular differentiation and developmental processes at single-cell resolution.
• Disease modeling and therapeutic target identification: Identifies pathways and genes whose trajectory-associated dynamics may indicate disease mechanisms or potential therapeutic targets.
• Regenerative medicine and cell-fate studies: Characterizes timing and coordination of pathway activation relevant to reprogramming, regeneration, or directed differentiation.

Methodology:

Integrates scRNAseq data with functional pathway knowledgebases and curated gene lists, maps developmental trajectories, assesses pathway significance, identifies pathway-associated genes, and analyzes timing of pathway activity changes.