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

Table 2 Summary of ModuleMiner's results for the ten microarray clusters

Cluster	Annotation	TFBS set	Number of target genes after cross-validation (P)	AUC on target genes	Number of target genes in independent test set (P)	Total number of CRMs
1	Protein synthesis	1	10/50 (0.025)	0.96	14/123 (0.35)	30
2	Oocyte/fertilized egg	3	10/50 (0.025)	0.98	30/164 (8.6 × 10^-4)	43
3	Neural tissues	3	10/50 (0.025)	0.84	15/122 (0.24)	29
4	Lymphocytes	3	10/50 (0.025)	0.87	23/85 (7.0 × 10^-6)	36
5	Testis/spermatogenesis	-	-	-	-	-
6	Liver	3	14/50 (2.9 × 10^-4)	0.93	7/29 (0.022)	23
7	Mitochondrion	3	9/31 (0.0026)	0.87	-	12
8	Extracellular matrix	2	7/32 (0.036)	0.92	-	10
9	Cardiac muscle	3	17/32 (6.6 × 10^-10)	0.95	-	16
10	Energy metabolism	3	7/26 (0.012)	0.82	-	10

Transcription factor binding site (TFBS) sets: set 1 includes 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 in which 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 were ranked within the top 10% of the genome where considered target genes of the transcriptional regulatory global model (TRGM). The total number of CRMs constitutes all successful CRM predictions near to genes in the cluster. CRM predictions were considered successful if the TRGM score was sufficient to rank the target gene within the top 10% of the genome. In some cases, multiple CRMs are found that control the same target gene.

ISSN: 1474-760X