Pyicoteo

Pyicoteo analyzes high-throughput sequencing (HTS) datasets, including ChIP-Seq (punctuated and broad signals), CLIP-Seq, and RNA-Seq, to quantify differential enrichment between conditions and model chromatin-mediated gene regulation.

Key Features:

• Multi-HTS Data Support: Processes ChIP-Seq, CLIP-Seq, and RNA-Seq datasets to analyze protein–DNA/RNA interactions and RNA expression levels.
• Differential Enrichment Analysis: Calculates differential enrichment between two conditions for CLIP-Seq and ChIP-Seq data, with or without replicates, to detect significant changes in binding or signal intensity.
• Epigenetic Data Integration: Integrates HTS epigenetic datasets to construct quantitative models of gene regulation and compare chromatin signals across cellular conditions.
• Alternative Splicing Analysis: Uses machine learning to identify chromatin signals associated with alternative splicing events involving CTCF, AGO1, and HP1.
• Enhancer Prediction: Applies a semi-supervised method to predict active transcriptional enhancers, including intragenic enhancers, based on relative chromatin signal enrichment between conditions.

Scientific Applications:

• Regulatory Network Analysis: Characterizes protein–DNA/RNA interactions and RNA expression to elucidate gene regulatory networks.
• Epigenetic Code Investigation: Integrates chromatin signals to study epigenetic mechanisms underlying gene regulation, cellular differentiation, and disease.
• Splicing Regulation Studies: Examines chromatin-associated regulation of alternative splicing and its relevance to splicing-related disorders.
• Enhancer Activity Profiling: Identifies differentially activated enhancers between cell types and evaluates their impact on host gene expression and splicing.

Methodology:

Employs memory-efficient computational algorithms for HTS signal selection and integration, differential enrichment analysis, and quantitative modeling of regulatory genomics, and incorporates machine learning and semi-supervised approaches to detect chromatin patterns associated with splicing and enhancer activity.