Table 2. Summary of model predictions and experimental validationsa
Prediction classSpecific PredictionValidationLocation
Accuracy of de novo discovery of GREs337 GREs discovered and genome‐wide locations predicted in E. coliPredictions validated by genome‐wide binding location data for 53 out of 88 characterized TFsFig 2A, Supplementary Dataset S2
Organization and composition of GREs within H. salinarum kdp promoterIn vivo transcription assays of truncated promoter constructsFig 2C
Organization and composition of GREs within E. coli carA promoterTF‐binding locations within the carA promoter (RegulonDB)Fig 2D
ArgR and PurR binding sites in E. coli pyrL promoterTF‐binding locations mapped using ChIP‐chip Supplementary Fig S18
Accuracy of TF–target interactions in the global GRNRegulatory interactions between 132 TFs and 1,131 genes in E. coli555 interactions correct at 25% precision, RegulonDBFig 2A
Regulatory mechanisms at non‐canonical promoter locations98 H. salinarum operons with condition‐specific transcript isoforms40 confirmed by tiling arraySupplementary Figs S19, S20 and S21, Supplementary Dataset S6
189 E. coli operons with condition‐specific isoforms58 confirmed by tiling arraySupplementary Figs S11, S12 and S13, Supplementary Dataset S6
Conditional isoforms of H. salinarum dpp operonTiling array and binding locations for TFBsFig 3, Supplementary Figs S22, S23, S24 and S25
Conditional regulation of branch points within metabolic pathwaysSegmentation of nucleotide biosynthesis pathway by multiple TFsCondition‐specific co‐expression; TF effector molecule correlation; Condition‐specific fitness consequences of gene deletionsFig 4, Supplementary Figs S26, S27, S28, S29, S30
Physiological consequences of deleting genes within coremsCorems establish a better relationship between co‐regulation and fitnessDeleting genes within corems result in similar fitness consequences in chemical genomics screenFig 2B and Supplementary Fig S14
Similar action by different TFs results in co‐regulation of genes across regulonsHighly correlated fitness effects of deleting genes within the same corem, albeit from different regulonsTable 1, Supplementary Fig S30, Supplementary Datasets S4 and S5
Regulation by a TF varies conditionally across different targets in the genomeDegree of PurR influence on regulation of its target genes across different coremsIncreased RSD in ∆purR/WT strains proportional to PurR influenceFig 5C
  • a All validations were performed with data from experiments that were not used in model construction.