Skip to main content

Advertisement

Table 5 CrmMiner performance on 57 human tissues and cell types

From: Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs

Tissue E-value h P-value Pairs The Three Most Enriched Pairs
subthalamic nucleus 6.72 2.1e −10 78 E2F1-TFIII E2F1DP2-ZBED6 GAF-NFMUE1
prefrontal cortex 6.60 5.7e −15 58 SP1-PITX3 PAX4-BEN EFC-E2A
cingulate cortex 6.44 4.3e −13 37 MAZR-NFAT2 PAX9-IK3 HEB-AHRARNT
heart 5.52 4.4e −20 89 PAX9-PXRRXR RSRFC4-E47 CETS1P54-NRSE
caudate nucleus 5.27 5.6e −14 20 SP1SP3-SP1 SP1-ETF MZF1-TAXCREB
prostate 5.03 4.2e −8 79 E2F-UF1H3BETA NFY-AP2GAMMA MSX3-SP3
amygdala 4.61 7.3e −10 34 ZFP281-RFX AHR-CKROX ETF-SP4
BM-CD71+ early erythroid 4.56 1.5e −8 90 PAX4-NRF1 NFY-KROX MOVOB-NFAT2
adrenal gland 4.40 5.7e −7 71 STAT6-ZF5 SP1-GATA3 NKX11-SP4
fetal brain 4.26 5.2e −15 90 VDR-E2F1 OBOX2-PPARA BEN-ETF
bone marrow 4.16 1.8e −7 68 CDXA-SP1 NFKB-E2F1 AR-PR
BM CD34+ 4.15 6.0e −9 130 NRSE-E2F1 E2F1-SP1 E2F-SP1
fetal thyroid 4.13 5.3e −8 108 E2F-SP4 NFY-ZF5 STAT3-MEF2
bronchial epithelial cells 4.09 7.4e −7 85 HOXD3-CEBP KLF15-CEBP NKX25-HEN1
occipital lobe 4.09 6.4e −4 38 EGR2-DEAF1 AHR-CACCCBINDINGFACTOR E2F1-SREBP
whole brain 4.05 3.5e −12 21 MAZ-ETF SP1SP3-GKLF MZF1-CTCF
PB-BDCA4+ dentritic cells 4.04 2.3e −9 98 ATF1-ETF AP1-PEBP AP2-PPARA 1
placenta 3.82 1.6e −11 96 COMP1-GKLF GKLF-NFY CTCF-AP1
hypothalamus 3.82 5.3e −5 80 GADP-ERR1 AP1-FOXO1 OCT-PAX5
liver 3.73 5.7e −9 97 COUP-SZF11 COUPTF-SRF GATA4-GFI1
thyroid 3.65 8.6e −8 93 MTATA-OLF1 MUSCLE-CHX10 LBX2-SP4
thymus 3.65 5.0e −7 93 IK1-KLF15 MINI19-ALPHACP1 IK1-GKLF
spinal cord 3.64 1.5e −6 68 IRF-LRF REX1-GLI3 ALPHACP1-PPARA
uterus 3.58 2.9e −8 85 ELK1-UF1H3BETA TAL1-E2F1 AP2ALPHA-PITX1
pons 3.57 6.1e −5 108 IPF1-CART1 NMYC-CNOT3 PAX4-MYOGNF1
trachea 3.48 1.1e −9 110 TRF1-TFIII DEC-CP2 COUPTF-STAT4
lung 3.47 3.0e −7 36 AP2-TR4 MAZ-CBF SP1SP3-AP1
tonsil 3.42 0.0019 60 HEN1-NFKAPPAB65 PAX4-SMAD E2F6-NRSF
PB-CD19+ Bcells 3.40 9.5e −8 61 ESE1-PAX6 PAX4-TBX5 MZF1-NRF2
721 B lymphoblasts 3.35 1.8e −6 104 SP1SP3-E2F4DP1 STAT4-NRF2 ZIC1-EGR1
testis 3.30 4.8e −4 73 AP2-ATF T3R-HNF4 MYOD-SRF
uterus corpus 3.27 1.3e −8 91 TCF4-POU6F1 CAAT-PITX3 PAX4-XVENT1
tongue 3.24 3.8e −7 72 ZFP281-NFY SP3-PITX3 AP2-IK2
temporal lobe 3.21 3.7e −7 95 TBX5-MTF1 MTATA-HIC1 ERG-ZIC3
PB-CD56+ NKCells 3.12 3.1e −5 53 NFY-SP1 CMYB-STAT6 SRF-SP4
smooth muscle 3.11 2.9e −6 87 KROX-MEF2 SP1-XBP1 HIF1-IK
pituitary gland 3.06 2.2e −6 96 MTATA-MAZR ZF5-WT1 AHR-ETF
adrenal cortex 3.04 1.5e −5 111 MYCMAX-PAX4 SP2-E2F1 VJUN-ZNF219
BM-CD105+ endothelial 2.95 0.0049 79 E2F-SMAD4 AP4-PAX4 P53-NFY
lymph node 2.94 2.6e −5 131 CETS1P54-GABP HIF1-NRSE PEA3-MTF1
adipocyte 2.91 1.3e −6 79 AP2-NFY E2F1-LXR CNOT3-IK2
skeletal muscle 2.89 7.6e −7 80 P53-CACD MEIS2-STAT1 MYOD-XVENT1
thalamus 2.86 0.0065 42 PLAG1-PAX3 AP1-CMAF MZF1-GATA2
pancreatic islets 2.79 6.7e −8 97 CDXA-PROP1 MEIS1-ZBED6 NFKB-E2F
skin 2.79 7.8e −5 73 CACBINDINGPROTEIN-XVENT1 NFKB-ZTA ER-SREBP1
medulla oblongata 2.78 7.9e −7 103 ZNF515-NKX25 CETS1P54-NKX26 P53-CMYB
whole blood 2.77 5.8e −5 53 PU1-SP2 GFI1-CTCF AP2-GR
cardiac myocytes 2.69 9.1e −4 120 EGR-MECP2 SRY-CNOT3 E2F-EGR3
fetal lung 2.62 1.7e −4 55 HIF1-LMAF CTCF-MECP2 AML2-CP2
PB-CD4+ Tcells 2.58 0.0026 121 NGFIC-EGR3 ZFP206-CBF AHRARNT- COUP
cerebellum peduncles 2.52 1.2e −4 74 ZNF219-NFY KLF15-OBOX2 NKX11-ZNF219
olfactory bulb 2.31 4.3e −4 70 NFY-SP1 NFKAPPAB-CTCF CP2-GLI
cerebellum 2.30 0.0034 58 AP2-LBX2 COUPTF-E2F E2F-SREBP
kidney 2.29 4.08e −5 87 GCM-ARP1 E2A-RORBETA NFY-TFIII
BM-CD33+ myeloid 1.80 0.0489 92 SRF-HMGIY PR-STAT6 T3R-AP1
parietal lobe 1.78 0.0443 82 AP2ALPHA-E2F1 HIF1-GABP BEN-MYF
appendix 1.75 0.0285 88 AP1-LXR PAX2-PAX4 CNOT3-CREB
  1. We trained, validated and tested CrmMiner on 72 human tissues and cell types [36]. The mixed sets consisted of CNEs in the vicinity of 160 tissue-specific genes. Those CNEs were located within 10 kbp up or downstream of the TSSs, or were among the closest 20 CNEs to the TSSs. Here, we report CrmMiner performance on the testing sets. The number of motif pairs comprising the tissue-specific signatures are listed under the Pairs column. The P-values were obtained by one-tailed Fisher's exact test.