Code - Cisregul (prediction of cis regulatory elements)

Transcriptional regulation in eukaryotes

Supplementary material and resources from "Identification of sparsely distributed clusters of cis regulatory elements in sets of co-expressed genes" by Gabriel Kreiman

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 3: Occurrences in the whole yeast genome of the module shown in Supplemental figure 3

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 1: Saturation of the number of non-redundant motifs in successive iterations of motif search programs

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

Overall strategy


Set of potentially coregulated genes


Single motifs

Motif scanning

Preliminary search for modules

Module enrichment



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

5. Resources

All the code is available upon request from the author

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