NAR Molecular Biology Database Collection entry number 1036
Jegga A.G.1,2, Chen J.1,3, Gowrisankar S.1,3, Deshmukh M.A.1, Gudivada R.1,3, Kong S.1, Kaimal V.1,3 and Aronow B.J.1,2,3
1Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 2Department of Pediatrics, College of Medicine, and 3Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45229, USA

Database Description

Adopting a systematic gene-centric pipeline approach, GenomeTraFaC ( allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.


This work was supported by grants NCI UO1 CA84291-07 (Mouse Models of Human Cancer Consortium), NIEHS ES-00-005 (Comparative Mouse Genome Centers Consortium) and NIEHS P30-ES06096 (Center for Environmental Genetics).

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