Supplementary material and resources from "Identification of sparsely distributed clusters of cis regulatory elements in sets of co-expressed genes"
Center for Biological and Computational Learning
McGovern Institute for Brain Research
Massachusetts Institute of Technology
1. Tables and figures refered to in the text
3. Performance on random sets of genes
4. Performance on known regulatory models
1. Tables and figures refered to in the text
Supplemental table 1: Performance on random sets of mouse genes, masked sequences
Supplemental table 2: Performance on random sets of mouse genes, unmasked sequences
Supplemental table 4: Occurrences in the whole fly genome of the module shown in Figure 2
Supplemental table 5: Occurrences in the whole human genome of the module shown in Figure 3
Supplemental figure 2: False alarm rate as a function of the propotion of genes with hits
Supplemental figure 3: Top module found for the CLB2 cluster in yeast
2. Methods
Set of potentially coregulated genes
Preliminary search for modules
3. Performance on random sets of genes
4. Performance on known regulatory models
4a Analysis of the clb2 set in yeast
4b Analysis of the pattern generation set in the fly
4c Analysis of the muscle regulatory regions in humans
All the code is available upon request from the author
We would like to thank Tommy Poggio, in whose lab the work was conducted. We would also like to thank John Hogenesch and Sayan Mukherjee for advice and Uwe Ohler and Mariela Zirlinger for discussion and comments on the manuscript. G.K. is supported by a Whiteman Fellowship at MIT.
last udpdated: 04-25-2004