The file AllUnconfirmedTargetsRanked.xls contains a spreadsheet with the columns corresponding to TFs. Genes are ordering from most likely to least likely of being a new target for the TF based on the semi-supervised method that uses expression data, motif information, and knowledge of genes with curated direct evidence. Genes which already have direct evidence of being regulated by the TF curated in EcoCyc 11.5 are excluded from this list. An entry in a cell is "gene|predictedsign" where "gene" is the blattner number of the gene and predictedsign is '+' if the TF primarily serves as an activator of the gene and '-' if the TF primarily serves as a repressor.

The file TopPredictions.xls is the subset of predictions from AllUnconfirmedTargetsRanked.xls that was used in the Aerobic-Anaerobic application. The number of new predictions is equivalent to the number of genes wtih confirmed direct evidence.

The file ConfirmedTargets.xls contains those TF-gene interactions supported by direct evidence in EcoCyc 11.5. The file is organized into columns by TFs as the files above. The format of an entry is "gene|predictedsign|annotatedsign", where the presence of the entry in gene in a column implies direct evidence the TF regulates the gene. predictedsign is defined as above, while for annotatedsign a '+' means only a curated direct evidence activator relationship, a '-' means only a curated direct evidence repressor relationship, otherwise the sign is '+-'. Genes are ordered using the same method as used to order new predictions.