BHE40.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	BHE40.H12RSNP.0.PSM.A
Gene (human)	BHLHE40 (GeneCards)
Gene synonyms (human)	BHLHB2, DEC1, SHARP2, STRA13
Gene (mouse)	Bhlhe40
Gene synonyms (mouse)	Bhlhb2, Clast5, Dec1, Stra13
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	ndGTCACGTGAbn
GC content	56.65%
Information content (bits; total / per base)	16.321 / 1.255
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9506

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	5 (35)	0.884	0.932	0.827	0.892	0.844	0.893	3.293	3.952	266.959	425.553
Mouse	7 (43)	0.897	0.959	0.818	0.927	0.837	0.925	3.2	4.496	222.602	438.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.999	0.998	0.99	0.988	0.871	0.88
Overall, 10 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999
Methyl HT-SELEX, 2 experiments	median	0.995	0.991	0.954	0.948	0.817	0.825
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.961	0.959	0.827	0.835
Non-Methyl HT-SELEX, 8 experiments	median	0.999	0.998	0.997	0.996	0.932	0.94
Non-Methyl HT-SELEX, 8 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	15.785	25.718	0.367	0.293

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	Hairy-related {1.2.4} (TFClass)
TF subfamily	HAIRY {1.2.4.1} (TFClass)
TFClass ID	TFClass: 1.2.4.1.12
HGNC	HGNC:1046
MGI	MGI:1097714
EntrezGene (human)	GeneID:8553 (SSTAR profile)
EntrezGene (mouse)	GeneID:20893 (SSTAR profile)
UniProt ID (human)	BHE40_HUMAN
UniProt ID (mouse)	BHE40_MOUSE
UniProt AC (human)	O14503 (TFClass)
UniProt AC (mouse)	O35185 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 7 mouse
HT-SELEX	8
Methyl-HT-SELEX	2

PCM	BHE40.H12RSNP.0.PSM.A.pcm
PWM	BHE40.H12RSNP.0.PSM.A.pwm
PFM	BHE40.H12RSNP.0.PSM.A.pfm
Alignment	BHE40.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	BHE40.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	BHE40.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	BHE40.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	BHE40.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	BHE40.H12RSNP.0.PSM.A_homer_format_0.001.txt BHE40.H12RSNP.0.PSM.A_homer_format_0.0005.txt BHE40.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2654.0	1874.0	2542.0	2436.0
02	2729.25	1180.25	4296.25	1300.25
03	963.0	231.0	8112.0	200.0
04	3.0	8.0	539.0	8956.0
05	7.0	9486.0	11.0	2.0
06	9505.0	0.0	0.0	1.0
07	0.0	9505.0	0.0	1.0
08	0.0	0.0	9506.0	0.0
09	1.0	8.0	0.0	9497.0
10	10.0	8.0	9457.0	31.0
11	7550.0	1547.0	188.0	221.0
12	605.25	3748.25	2177.25	2975.25
13	1904.0	2432.0	3152.0	2018.0

PFM

	A	C	G	T
01	0.279	0.197	0.267	0.256
02	0.287	0.124	0.452	0.137
03	0.101	0.024	0.853	0.021
04	0.0	0.001	0.057	0.942
05	0.001	0.998	0.001	0.0
06	1.0	0.0	0.0	0.0
07	0.0	1.0	0.0	0.0
08	0.0	0.0	1.0	0.0
09	0.0	0.001	0.0	0.999
10	0.001	0.001	0.995	0.003
11	0.794	0.163	0.02	0.023
12	0.064	0.394	0.229	0.313
13	0.2	0.256	0.332	0.212

PWM

	A	C	G	T
01	0.11	-0.237	0.067	0.025
02	0.138	-0.699	0.592	-0.602
03	-0.902	-2.322	1.227	-2.465
04	-6.109	-5.443	-1.48	1.326
05	-5.545	1.383	-5.187	-6.318
06	1.385	-6.946	-6.946	-6.583
07	-6.946	1.385	-6.946	-6.583
08	-6.946	-6.946	1.386	-6.946
09	-6.583	-5.443	-6.946	1.385
10	-5.266	-5.443	1.38	-4.269
11	1.155	-0.429	-2.526	-2.366
12	-1.365	0.455	-0.087	0.225
13	-0.221	0.023	0.282	-0.163

Standard thresholds

P-value	Threshold
0.001	-0.88004
0.0005	1.008915
0.0001	4.76446