In an effort to aid scientists in locating gene promoters, a team from the Wistar Institute has released an online tool — the Mammalian Promoter Database, or MPromDb — that integrates a range of publicly available human and mouse genomic data. This new Web interface allows researchers to pinpoint known promoters, and predicts which are most likely to be located by mining databases like Gene Expression Omnibus and the ENCyclopedia of DNA Elements, as well as Wistar's own public genomics data. MPromDb aims to provide an in silico platform for studies that focus on mammalian transcriptional regulation and epigenomics.
"Scientists are so good at generating this sort of information using the next-generation sequencing methods that they collect information far in excess of what they might need for a given experiment or project. This information all ends up in places like NCBI GEO or UCSC Genome [Browser] databases, waiting to be discovered by groups like ours," says Ramana Davuluri, associate director of Wistar's Center for Systems and Computational Biology. "We are currently processing epigenetic histone modification profiles identified from ChIP-seq data sets and integrating it to MPromDb promoter knowledge base." The tool's developers are now collecting RNA polymerase II and transcription factor binding ChIP-seq data sets from a wide variety of tissues and cell types to update their database.
Davuluri and his team say they envision MPromDb as a way to enable researchers to search for tissue, cell, or developmental stage-specific promoter of a gene of interest in order to make new discoveries. "They can search for known histone modification profiles and transcription factor binding sites mostly curated from ChIP-seq data sets in specific gene promoters," Davuluri says. "This can lead to important discoveries about gene regulation, such as the epigenetic state of gene promoters of interest, as well as the direct target promoters or genes or a transcription factor of interest in a given cell or tissue type. The integrated resource can therefore be used to discover sets of novel cell- or tissue type-specific molecular markers."