EPD

EPD provides comprehensive experimentally validated transcription start site (TSS) annotations for eukaryotic promoters across multiple model organisms.

Key Features:

• Comprehensive TSS Collections: Organism-specific TSS collections derived from CAGE, TSS-seq, GRO-cap, and RAMPAGE high-throughput sequencing for precise TSS mapping.
• Integration with Functional Genomics Data: Integration of promoter-relevant chromatin profiling and ChIP-seq datasets with high-resolution CAGE tracks and public track hubs for genome browsers such as the UCSC Genome Browser.
• Data Accessibility and Export Options: Data export in FASTA, BED, and CSV formats and numeric promoter-associated data extraction via the ChIP-Extract tool for downstream analysis in platforms like R.
• Enhanced Visualization and Querying: Customized, reproducible combinations of EPD-supplied and native UCSC Genome Browser tracks for promoter-centered visualization.
• Expansion to Additional Organisms and ncRNAs: Expanded promoter collections including rhesus monkey, rat, dog, chicken, and Plasmodium falciparum, plus promoter sets for certain classes of human and mouse ncRNAs.
• Automatic Assignment Protocols: Automatic computational protocols that assign orphan TSS peaks to downstream genes using paired-end TSS mapping data, adding nearly 9,000 human promoter entries.

Scientific Applications:

• Gene regulation and expression: Identification and characterization of promoter regions and regulatory elements involved in transcription initiation.
• Transcriptional biology: Analysis of transcription start site usage, promoter architecture, and initiation mechanisms.
• Epigenetics and chromatin regulation: Correlation of promoter activity with chromatin marks and transcription factor binding from ChIP-seq and chromatin profiling data.
• Comparative genomics: Comparison of promoter architectures and TSS patterns across multiple eukaryotic species, including newly added organisms.
• Non-coding RNA regulation: Investigation of promoter usage and regulatory contexts of classes of ncRNAs in human and mouse.

Methodology:

Compilation and annotation of TSSs from NGS datasets (CAGE, TSS-seq, GRO-cap, RAMPAGE), integration of ChIP-seq and chromatin profiling data, generation of high-resolution genome browser tracks and public track hubs, automatic assignment of orphan TSS peaks to downstream genes using paired-end TSS mapping data, and numerical extraction of promoter-associated signals via ChIP-Extract.