Key Personnel:
Ramana V. Davuluri (PI)
Tim Huang (Co-I)
Christoph Plass (Co-I)
Pearlly Yan (Co-I)
Hao Sun, Research Scientist
Sandya Liyanarachichi, Statistics Specialist
Gregory Singer, Post doctoral Researcher
Yi-Wen Huang, Post doctoral Researcher
Priyankara Wickramasinghe, Post doctoral Researcher
Promoters located at the 5'-ends of genes play a critical role in regulating transcriptional initiation. Emerging evidence suggests that a significant fraction of ~35,000 genes in the human genome likely contain alternative promoters, which produce more elaborate regulation of gene expression in different tissues, cell-types and/or developmental stages. Despite vast information available for the human genome sequences, a comprehensive approach for identifying and characterizing alternative promoters of gene loci is still lacking.
We are currently utilizing comparative genomics approaches in combination with pattern recognition methods to analyze the 5'end functional regions of orthologous human and mouse genes. We are collaborating with the laboratory of Tim Huang of Human Cancer Genetics, OSU to experimentally validate our computational predictions, by utilizing Chip-on-chip assays. The combination of computational, statistical and high throughput experimental approaches will, hopefully, contribute toward the characterization of alternative promoters and first exons in the human genome.
In order to integrate the immense amount of available data, we have developed
an efficient data-mining pipeline that integrates important details about
several gene promoters and the expression pattern of corresponding genes
with the genome sequences. We have deposited all this information in a database
composed of a genome-wide map of mammalian promoters and first exons, entitled
MpromDb: The Mammalian Promoter Database. Additional information and access
to the user-friendly web interface may be accessed from:
http://bioinformatics.wistar.upenn.edu/MPromDb.
Sponsored by: The National Human Genome Research Institute