THA.H12RSNP.0.P.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	THA.H12RSNP.0.P.D
Gene (human)	THRA (GeneCards)
Gene synonyms (human)	EAR7, ERBA1, NR1A1, THRA1, THRA2
Gene (mouse)	Thra
Gene synonyms (mouse)	C-erba-alpha, Nr1a1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	17
Consensus	vRGGKSRnnYvAGGhSA
GC content	57.24%
Information content (bits; total / per base)	13.629 / 0.802
Data sources	ChIP-Seq
Aligned words	1000

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	1 (6)	0.922	0.966	0.888	0.935	0.95	0.984	5.558	6.735	78.678	275.0
Mouse	2 (12)	0.919	0.951	0.876	0.907	0.914	0.946	4.427	4.539	408.165	461.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.619	0.593	0.577	0.561	0.542	0.539
Non-Methyl HT-SELEX, 2 experiments	best	0.65	0.618	0.604	0.58	0.557	0.552

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	Thyroid hormone receptor-related {2.1.2} (TFClass)
TF subfamily	T3R (NR1A) {2.1.2.2} (TFClass)
TFClass ID	TFClass: 2.1.2.2.1
HGNC	HGNC:11796
MGI	MGI:98742
EntrezGene (human)	GeneID:7067 (SSTAR profile)
EntrezGene (mouse)	GeneID:21833 (SSTAR profile)
UniProt ID (human)	THA_HUMAN
UniProt ID (mouse)	THA_MOUSE
UniProt AC (human)	P10827 (TFClass)
UniProt AC (mouse)	P63058 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 2 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	THA.H12RSNP.0.P.D.pcm
PWM	THA.H12RSNP.0.P.D.pwm
PFM	THA.H12RSNP.0.P.D.pfm
Alignment	THA.H12RSNP.0.P.D.words.tsv
Threshold to P-value map	THA.H12RSNP.0.P.D.thr
Motif in other formats
JASPAR format	THA.H12RSNP.0.P.D_jaspar_format.txt
MEME format	THA.H12RSNP.0.P.D_meme_format.meme
Transfac format	THA.H12RSNP.0.P.D_transfac_format.txt
Homer format	THA.H12RSNP.0.P.D_homer_format_0.001.txt THA.H12RSNP.0.P.D_homer_format_0.0005.txt THA.H12RSNP.0.P.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	284.0	196.0	393.0	127.0
02	521.0	22.0	441.0	16.0
03	91.0	4.0	866.0	39.0
04	45.0	12.0	830.0	113.0
05	32.0	109.0	230.0	629.0
06	30.0	720.0	126.0	124.0
07	807.0	54.0	79.0	60.0
08	162.0	235.0	292.0	311.0
09	171.0	381.0	224.0	224.0
10	38.0	304.0	70.0	588.0
11	226.0	267.0	427.0	80.0
12	745.0	5.0	241.0	9.0
13	0.0	0.0	995.0	5.0
14	7.0	9.0	966.0	18.0
15	469.0	167.0	71.0	293.0
16	44.0	794.0	92.0	70.0
17	836.0	48.0	61.0	55.0

PFM

	A	C	G	T
01	0.284	0.196	0.393	0.127
02	0.521	0.022	0.441	0.016
03	0.091	0.004	0.866	0.039
04	0.045	0.012	0.83	0.113
05	0.032	0.109	0.23	0.629
06	0.03	0.72	0.126	0.124
07	0.807	0.054	0.079	0.06
08	0.162	0.235	0.292	0.311
09	0.171	0.381	0.224	0.224
10	0.038	0.304	0.07	0.588
11	0.226	0.267	0.427	0.08
12	0.745	0.005	0.241	0.009
13	0.0	0.0	0.995	0.005
14	0.007	0.009	0.966	0.018
15	0.469	0.167	0.071	0.293
16	0.044	0.794	0.092	0.07
17	0.836	0.048	0.061	0.055

PWM

	A	C	G	T
01	0.127	-0.241	0.45	-0.671
02	0.731	-2.362	0.565	-2.653
03	-0.999	-3.783	1.238	-1.821
04	-1.684	-2.909	1.195	-0.786
05	-2.01	-0.821	-0.083	0.919
06	-2.071	1.053	-0.678	-0.694
07	1.167	-1.508	-1.137	-1.406
08	-0.43	-0.061	0.154	0.217
09	-0.377	0.419	-0.109	-0.109
10	-1.846	0.194	-1.255	0.851
11	-0.1	0.065	0.532	-1.125
12	1.087	-3.622	-0.036	-3.156
13	-4.982	-4.982	1.376	-3.622
14	-3.362	-3.156	1.347	-2.546
15	0.626	-0.4	-1.242	0.158
16	-1.706	1.151	-0.988	-1.255
17	1.202	-1.622	-1.39	-1.49

Standard thresholds

P-value	Threshold
0.001	3.67806
0.0005	4.72991
0.0001	6.90516