Modules    GeneXPress

   Global Analysis (Fig. 3)    Experimental Tests    Candidate Regulators

   Technical Reports



   Supplemental Information

Regulators Analysis

To analyze the regulators associated with each of the modules, we examined the set of genes in all the modules regulated by each regulator and evaluated that set using the following sources:
  • Functional gene annotations (Gene Ontology, MIPS and KEGG)
  • Motif binding sites (known motifs from TRANSFAC and de-novo motifs learned using a method previously published by Segal, Barash, Simon, Friedman and Koller in RECOMB 2002)
  • Protein-DNA binding assays published in Lee et al, Science...
Each square in the regulator-annotation matrix corresponds to the fraction of genes in all modules regulated by the regulator that have that annotation. p-values were computed (correcting for multiple hypotheses) and significant events were colored in shades of orange and insignificant events in shades of blue (using a significance level of 0.05). We show the full matrices as well as matrices filtered for only the significant events as well as matrices where only informative annotations were kept.