COTAN

COTAN analyzes the co-expression of gene pairs at single-cell level using a generalized contingency tables framework that studies zero UMI counts' distribution rather than positive counts, providing the foundation for single-cell gene interactome analysis.

Key Features:

• Co-expression Assessment: COTAN effectively assesses the correlated or anti-correlated expression of gene pairs, providing a numerical index related to the correlation and an approximate p-value for the associated independence test.
• Differential Expression Evaluation: COTAN evaluates whether single genes are differentially expressed, scoring them with a newly defined global differentiation index.
• Gene Clustering and Visualization: COTAN provides ways to plot and cluster genes according to their co-expression pattern with other genes.
• Marker Gene Identification: COTAN serves as a tool to identify cell-identity marker genes through the study of gene interactions.

Scientific Applications:

• Single-Cell Gene Interactome Analysis: COTAN provides the foundation for analyzing gene interaction networks at single-cell resolution.
• Gene Interaction Study: COTAN helps study gene interactions by clustering genes according to their co-expression patterns with other genes.
• Cell Identity Marker Discovery: COTAN identifies cell-identity marker genes through co-expression pattern analysis.

Methodology:

COTAN employs a generalized contingency tables framework that analyzes the distribution of zero UMI counts rather than focusing on positive counts to study co-expression of gene pairs at single-cell level.