Appendix 14 of Pratt, Mol Vis 2008; 14:1414-1428.

Appendix 14. Complete Candidate Interaction Matrix (CIM) for transcription response elements from PAINT analysis of rat gene promoters.

To access the data, click or select the words “Appendix 14.” This will initiate the download of a pdf archive that contains the file. The RPE gene set was analyzed by PAINT and a graphic CIM was generated as described in Methods. The y-axis lists the Ensembl Gene identifiers for each gene and the x-axis lists the TRANSFAC TRE identifiers for each TRE found at least once in the promoter region. Genes listed along the y-axis are divided into two clusters that are either up-regulated (blue) or down-regulated (green) during EMT of RPE cells. TREs listed along the x-axis are clustered according to related occurrence pattern calculated using Jaccard's coefficient. The elements within the matrix are color-coded based upon the p-value of each TRE found in the regulatory regions of the genes. A red dot represents a TRE that is statistically significant and therefore over-represented in our gene set, while a blue dot signifies an under-represented TRE and a grey dot stands for a TRE with no statistical significance in our gene list. Note: This is a large-format figure and should be viewed at enhanced magnification to read the text in specific sections of the figure.