title: MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.
abstract: MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-seq results with the goal of providing an integrated resource for mammalian transcriptional regulation and epigenetics. We analyzed 507 million uniquely aligned RNAP-II ChIP-seq reads from 26 different data sets that include six human cell-types and 10 distinct mouse cell/tissues. The updated MPromDb version consists of computationally predicted (novel) and known active RNAP-II promoters (42,893 human and 48,366 mouse promoters) from various data sets freely available at NCBI GEO database. We found that 36% and 40% of protein-coding genes have alternative promoters in human and mouse genomes and ∼40% of promoters are tissue/cell specific. The identified RNAP-II promoters were annotated using various known and novel gene models. Additionally, for novel promoters we looked into other evidences-GenBank mRNAs, spliced ESTs, CAGE promoter tags and mRNA-seq reads. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter results based on any combination of tissue/cell specificity, Known/Novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. We have also integrated GBrowse genome browser with MPromDb for visualization of ChIP-seq profiles and to display the annotations. The current release of MPromDb can be accessed at http://bioinformatics.wistar.upenn.edu/MPromDb/.
authors.affiliation: Center for Systems and Computational Biology, Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA.
authors.forename: Ravi
authors.initials: R
authors.lastname: Gupta
authors.forename: Anirban
authors.initials: A
authors.lastname: Bhattacharyya
authors.forename: Francisco J
authors.initials: FJ
authors.lastname: Agosto-Perez
authors.forename: Priyankara
authors.initials: P
authors.lastname: Wickramasinghe
authors.forename: Ramana V
authors.initials: RV
authors.lastname: Davuluri
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D017422:Sequence Analysis, DNA; D018511:Systems Integration
chemical_list: D012319:RNA Polymerase II