Heat seq

Heat seq performs genome-scale comparisons of high-throughput sequencing experiments to contextualize ChIP-seq, RNA-seq, and CAGE data against over 12,000 public datasets from human, mouse, and Drosophila.

Key Features:

• Supported data types: Comparison of ChIP-seq, RNA-seq, and CAGE experiments.
• Public dataset repository: Compares input experiments against a collection of over 12,000 publicly available datasets spanning diverse tissues and cell types from human, mouse, and Drosophila.
• Genome-wide comparisons: Performs genome-wide analyses rather than single-gene comparisons.
• Correlation heatmaps: Computes and visualizes correlation heatmaps to assess similarity between experiments.
• Dynamic subsetting: Enables dynamic subsetting of datasets to focus analysis on specific regions or conditions.
• Exportable summaries: Produces figures and tables summarizing genome-wide comparisons.

Scientific Applications:

• Contextualization of experiments: Places new sequencing experiments in the context of public data to aid biological interpretation.
• Comparative tissue and cell-type analysis: Compares profiles across diverse tissues and cell types in human, mouse, and Drosophila.
• Benchmarking and quality assessment: Assesses similarity to reference experiments for dataset quality control and benchmarking.
• Regulatory landscape analysis: Facilitates genome-wide comparison of chromatin features from ChIP-seq datasets.
• Expression profiling comparisons: Enables comparative analysis of expression patterns from RNA-seq and CAGE data.

Methodology:

Computes genome-wide correlations between input high-throughput experiments and public datasets and visualizes the results as interactive correlation heatmaps with dynamic dataset subsetting.