Mammalian Promoter Database (MPromDb)

Mammalian Promoter Database (MPromDb) annotates promoters identified from Chromatin Immunoprecipitation sequencing (ChIP-seq) data to catalogue RNA Polymerase II (RNAP-II)–bound promoters across human and mouse cell types and tissues.

Key Features:

• Extensive dataset integration: Incorporates 507 million uniquely aligned RNA Polymerase II (RNAP-II) ChIP-seq reads from 26 distinct datasets covering six human cell types and ten mouse tissues or cells.
• Promoter annotation: Contains 42,893 human and 48,366 mouse promoters, including computationally predicted novel promoters and known active RNAP-II promoters, annotated against multiple gene models and supported by GenBank mRNAs, spliced ESTs, CAGE promoter tags, and mRNA-seq reads.
• Alternative promoters: Identifies alternative promoters in approximately 36% of human protein-coding genes and 40% of mouse protein-coding genes.
• Tissue/cell specificity: Reports that around 40% of identified RNAP-II promoters exhibit tissue or cell specificity.

Scientific Applications:

• Transcriptional regulation and epigenetics: Enables investigation of transcriptional regulation and epigenetic modifications by cataloguing RNAP-II promoter occupancy.
• Gene expression and promoter functionality: Supports analysis of gene expression dynamics and promoter functionality across cell types and tissues.
• Regulatory network elucidation: Facilitates elucidation of regulatory networks across different tissues and developmental stages.
• Discovery of novel promoters and alternative splicing: Assists discovery of novel promoters, alternative promoter usage, and related alternative splicing events.

Methodology:

Annotations are derived from analysis of uniquely aligned RNAP-II ChIP-seq reads and promoter identification referenced to gene models, with supporting evidence from GenBank mRNAs, spliced ESTs, CAGE promoter tags, and mRNA-seq reads.