ROVER (Relative OVER-abundance of cis-elements) is a tool for determining if one or more of a group of transcription factors is likely to regulate a group of genes. It was designed for use with promoters from groups of genes that are suspected of being co-regulated, such as those from a microarray study. ROVER compares two groups of promoters (a suspected co-regulated group and a non-regulated group) by determining the relative over-abundance of likely binding sites for a particular Transcription Factor (TF) in one group versus the other. ROVER calculates the significance of any over-abundance of binding sites for each TF and reports a probability of its chance occurrence. This can be interpreted as the probability that a given TF regulates the group of genes in question. Likely binding sites are found by looking for high-scoring matches to a Position Specific Weight Matrix (PSSM), which represents known binding sites for a transcription factor. In addition to determining the significance of each TF, ROVER also provides the subset of sequences likely to be regulated by each TF and the specific significant binding sites.
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Haverty, PM., Hansen, U., Weng, Z. (2004) Computational Inference of Transcriptional Regulatory Networks from Expression Profiling and Transcription Factor Binding Site Identification. Nucleic Acids Research, Vol. 32, 179-188.