The rule-files list each rule and gives a table with annotations and transcription factors binding to genes matching the rule.

 

RULE: x y

 

Rule linking a binding site combination with the gene expression profile of a particular gene. x is the number of genes with similar expression to that particular gene, while y is the number of genes with non-matching profile.

 

EXPR

 

The expression tightness of the genes matching the rule in parentheses (Euclidean distance, normalized by the number of measurement points, between the central gene and the other genes) followed by P-values for the expression tightness for each single binding site.

 

|ORF|

 

Genes with a “different” expression profile are marked with ||.

 

P, F, C, TF

 

Biological process, molecular function, cellular component and transcription factors binding according to Lee et al (P < 0.01)

 

Gene Ontology annotations -> Gene Ontology annotations

 

The annotations before the arrow are original annotations, while the annotations after are propagated upwards in the Gene Ontology hierarchy to find common annotations among the genes matching the rule.

 

Main

 

The most frequently occurring annotation or transcription factor (fraction of genes with this annotation/transcription factor in parentheses).

 

Score

 

Fraction of gene-pairs with the same annotation or transcription factor.

 

P-value

 

The probability that the Gene Ontology term in parentheses were used to annotate that many genes matching this rule by chance (only the lowest P-value is given).

 

AVERAGE SCORES

 

Average for Main and Score computed over all rules. For P-value, the fraction of significant rules (P < 0.001) is given.