I am interested in finding transcription factors binding to promoter of a virus, Merkel cell polyomavirus. I got several factors with varying dissimilarity. Is there any criteria that can be used while selecting the tf's?
Hi Vrushail Kashinath,
Please read the paper of Oshchepkov D, Grigovich D, Ignatieva E, Khleborova T. (2004); in Nucleic Acids Res. 32:W208-12. That is because we have successfully used the SITECON approach to study transcriptional factor (namely, Ah receptor signaling complex) binding to viral promoter site DRE. In a nutshell, a total of 13 bona fide DREs, all including the substitution intolerant core sequence (5’-GCGTG-3’) and adjacent variable sequences, were used as a training sample to detect conservative conformational and physico-chemical properties for the site with DRE, and to construct the recognition rules and determine conformational similarity score threshold to rank identified DREs. We used the approach utilized for mammalian DREs, but the recognition threshold of 0.95, for which type I error equal to zero, i.e., the condition when SITECON employed conformational similarity score allowing recognize all sites in the training sample. Earlier, an efficacy of SITECON in detection of functionally active DREs was tested using sequences of genes encoding human CYP1A1 and CYP1B18, which was also proven experimentally. It was demonstrated that at the recognition threshold of 0.95, SITECON efficiently identified all tested functionally active DREs. In fact, promoter DREs within genes encoding AhR, HSP90, XAP2, and macrophage proinflammatory factors were detected by SITECON with high scores of 0.974-0.98.
Best wishes,
Ilya
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