refTSS

refTSS provides an integrated reference dataset of transcription start sites (TSSs) for human and mouse genomes to support analysis of gene expression regulation.

Key Features:

• Integrated annotations: Consolidates multiple publicly available TSS annotations and promoter databases including FANTOM5, DBTSS, EPDnew, and ENCODE.
• Genomic coordinates: Compiles genomic coordinates for TSS peaks across human and mouse genomes.
• Gene annotations: Supplies detailed gene annotations linked to TSS entries.
• Quality assessments: Provides quality assessments for TSS entries.
• Evolutionary conservation: Supplies evolutionary conservation insights between human and mouse genomes.
• Data integration for regulation and RNA production: Facilitates integration of datasets related to regulatory mechanisms and RNA production processes.

Scientific Applications:

• Gene expression regulation: Supports analyses of promoter usage and transcription initiation underlying gene expression regulation.
• Transcriptional dynamics: Enables study of transcriptional dynamics by providing unified TSS references.
• Comparative genomics: Enables evolutionary comparison of TSSs between human and mouse.
• Integration with regulatory datasets: Serves as a reference set for combining promoter and regulatory data to study transcriptional regulation and RNA products.

Methodology:

Consolidation and integration of publicly available TSS annotations and promoter databases (FANTOM5, DBTSS, EPDnew, ENCODE) to compile genomic coordinates of TSS peaks, generate gene annotations, perform quality assessments, and derive evolutionary conservation insights between human and mouse genomes.