Welcome to MPromDb
MPromDb (Mammalian Promoter Database) is a curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results. The long term goal of this database is to provide an integrated resource for mammalian gene transcriptional regulation and epigenetics.
In the latest version of MPromDb, we have analyzed 507 million uniquely aligned RNA Pol-II ChIP-seq reads from 26 different datasets. The datasets were downloaded from various published and unpublished works freely available at NCBI GEO database repository. Based on analyzed ChIP-seq datasets we found that 36% of protein-coding genes in human and 40% in mouse have alternative promoters. Annotation of identified promoters was performed using various known and novel gene models. Additionally, for novel promoters we looked into other evidences such as GenBank mRNAs, spliced ESTs, CAGE promoter tags and mRNA-seq reads.
Users can search databse based on Enterz gene id/symbol, or by tissue/cell specific activity and filter results based on any combination of tissue/cell specificity, known/novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. MPromDb is also integrated with GBrowse genome browser for visualiztion of ChIP-seq profiles and display the annotations.
MPromDb update 2010: An integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data
R. Gupta*, A. Bhattacharyya*, F. J. Agosto-Perez, P. Wickramasinghe and R. V. Davuluri.
Nucleic Acids Research, Vol. 39, D92-97, 2011. [Full Text] [PDF]
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
Hao Sun, Saranyan K. Palaniswamy, Twyla T. Pohar, Victor X. Jin, Tim H.-M. Huang and Ramana V. Davuluri.
Nucleic Acids Research, Vol. 34, D98-D103, 2006. [Full Text] [PDF] [PubMed]
Other Related Publications
Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
S. Pal*, R. Gupta*, H. Kim, P. Wickramasinghe, V. Baubet, L. C. Showe, N. Dahmane, and R. V. Davuluri.
Genome Research, 2011. [Abstract] [PubMed] [NCBI GEO] [Annotated_Data_Access]
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq
H. Sun*, J. Wu*, P. Wickramasinghe*, S. Pal*, R. Gupta*, A. Bhattacharyya, F. J. Agosto-Perez, L. C. Showe, T. H.-M. Huang and R. V. Davuluri.
Nucleic Acids Research, Vol. 39, pp. 190-201, 2011. [Full Text] [PDF] [PubMed] [NCBI GEO]
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
R. Gupta, P. Wikramasinghe, A. Bhattacharyya, Francisco A. Perez, S. Pal and R. V. Davuluri.
BMC Bioinformatics, Vol.11, 2010. [Full Text] [PDF] [PubMed]