MotifModeler is designed to identify cis-acting elements (CAE) from array-derived gene expression data and genomic DNA sequences.  MotifModeler repeatedly tests random subsets of all possible DNA elements of a fixed size in the regulatory region, and selecting those that best fit a combinatorial model of gene expression levels.  This online MotifModeler provides the following functionalities:

1. Identifying cis-acting elements that regulate gene expression under a given condition;
2. Estimating the effects of the CAE on gene expression;
3. Demonstrating the relationship between the predicted CAE and the position weight matrices of the experimentally-verified transcription factor binding sites in the TRANSFAC database.

For discussion and comments on MotifModeler and this website, please contact Dr. Yunlong Liu (yunliu@iupui.edu) in the Center for Computational Biology and Bioinformatics at Indiana University School of Medicine.

References:

Liu Y, Taylor MW, and Edenberg HJ. Model-based identification of cis-acting elements from microarray data. Genomics 2006 October;  88(4):452-61. Epub 2006 May 23.