Skip to main content

Table 3 Summary of ModuleMiner's results for the five embryonic development gene sets

From: ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

Embryonic development process TFBS set Number of target genes after LOOCV (P) AUC
Primary heart field [50] 1 6/7 (6.4 × 10-6) 0.92
Secondary heart field [50] 1 6/9 (6.4 × 10-5) 0.79
Neural crest cells [51] 2 6/10 (1.5 × 10-4) 0.86
Eye development [52] 1 10/15 (1.9 × 10-7) 0.79
Limb development [53] 1 10/24 (5.2 × 10-5) 0.77
  1. A key review or book used as a basis for construction of the development gene set is given in the first column. The genes in each set as well as the detailed results can be viewed at our website [26]. Transcription factor binding site (TFBS) sets: set 1 includes the human-mouse conserved noncoding sequences (CNSs) 10 kilobases 5' of the transcription start site (TSS); set 2 includes set 1 + binding site preservation; and set 3 includes set 2 + correction for TSS differences. For clusters where multiple TFBS sets resulted in successful cis-regulatory module (CRM) detection, only the result showing the best cross-validation performance is shown. Genes (in the cluster) that by cross-validation where ranked within the top 10% of the genome where considered target genes of the transcriptional regulatory global model. LOOCV, leave-one-out cross-validation.