Table 2

A selection of regions of local enrichment that could not be found using standard TFBS over-representation analysis
Tissues or cell types (cluster index) Transcription factor Region of enrichment: PORI References
x1 to x2 ( h/ 2)
B cells, T cells (2) ETS domain TFs, including SPI1 or PU.1 -10 to 0 (10) 0.15 [44,45]
B cells, T cells (2) HIF1 55 to 200 (200) 0.11 [46]
testis (10) RFX1 -91 to 129 (200) 0.012 [47,48]
testis (10) CREB-binding TFs, including ATF family -148 to 31 (100) 0.035 [49,50]
liver (16) Cux1 (CR3 + HD) -103 to -90 (10) 0.037 [51]
small and large intestine (19) HNF1 -93 to -37 (20) 0.012 [52]
small and large intestine (19) RXR, RAR, and VDR -52 to -43 (10) 0.065 [53,54]
testis (22) MYB family TFs -72 to 95 (100) 0.025 [55,56]
testis (22) heat shock factors -58 to 217 (200) 0.032 [57]
skeletal muscle (42) THR alpha and beta -30 to -15 (50) 0.025 [58,59]

A selection of regulatory motifs is shown for which regions of local enrichment were detected in mouse tissues and cell types of the GNF GeneAtlas dataset. The tissue, the start and stop position of the region, the h/2 used, the ORI p-value, and references supporting the role of the regulatory motif in the tissue in question are shown.

Vandenbon et al.

Vandenbon et al. BMC Bioinformatics 2013 14:26   doi:10.1186/1471-2105-14-26

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