Abstract
GENEACT, a new software suite for the detection of evolutionarily conserved transcription factor binding sites or microRNAs from differentially expressed genes from DNA microarray data, is described.
Highlights
Cell type and tissue specific gene expression patterns are primarily governed by the cis-regulatory sequence elements embedded in the noncoding regions of the genome
The levels of mRNA transcript can be modulated by microRNAs, which tend to bind specific sequences in the 3'-untranslated region (UTR) of the transcript
DNA microarray technology is used to profile relative mRNA transcript levels between samples exposed to different experimental conditions
Summary
GeneACT was developed to display and analyze regulatory regions across human, mouse and rat genomes, and it enables identification of putative cis-acting elements that are evolutionarily conserved across species for all orthologous genes. It is important to investigate both transcription factors and miRNAs when searching for critical genes that may be responsible for differential gene expression By integrating both transcription factor binding sites and miRNA target sites into DBSS, we provide a more comprehensive analysis of DNA microarray datasets. In the future we plan to add additional genomes to GeneACT as they become available Even so, it is possible for researchers interested in other species to use GeneACT by taking advantage of the input sequence feature and/or input binding site feature of PBSS. Additional data file 5 is a table containing the original DNA microarray data generated by Tomczak and coworkers [40] used for the DBSS; gene IDs of regulated and control gene sets used for the search are listed.
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