THB.H12RSNP.2.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	THB.H12RSNP.2.SM.D
Gene (human)	THRB (GeneCards)
Gene synonyms (human)	ERBA2, NR1A2, THR1
Gene (mouse)	Thrb
Gene synonyms (mouse)	Erba2, Nr1a2
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	D

Motif length	14
Consensus	RGGTCAAAGGTCAn
GC content	49.85%
Information content (bits; total / per base)	17.363 / 1.24
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9779

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 (7)	0.712	0.725	0.539	0.552	0.656	0.661	1.681	1.702	29.699	33.959
Mouse	1 (5)	0.53	0.541	0.353	0.358	0.464	0.47	0.976	0.978	1.409	1.523

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.851	0.78	0.82	0.751	0.776	0.716
Overall, 6 experiments	best	1.0	1.0	1.0	1.0	0.981	0.98
Methyl HT-SELEX, 2 experiments	median	0.921	0.885	0.904	0.869	0.871	0.839
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.997	0.996	0.977	0.973
Non-Methyl HT-SELEX, 4 experiments	median	0.71	0.662	0.687	0.644	0.656	0.623
Non-Methyl HT-SELEX, 4 experiments	best	1.0	1.0	1.0	1.0	0.981	0.98

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: 2.1.2.2.2
HGNC	HGNC:11799
MGI	MGI:98743
EntrezGene (human)	GeneID:7068 (SSTAR profile)
EntrezGene (mouse)	GeneID:21834 (SSTAR profile)
UniProt ID (human)	THB_HUMAN
UniProt ID (mouse)	THB_MOUSE
UniProt AC (human)	P10828 (TFClass)
UniProt AC (mouse)	P37242 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 1 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	THB.H12RSNP.2.SM.D.pcm
PWM	THB.H12RSNP.2.SM.D.pwm
PFM	THB.H12RSNP.2.SM.D.pfm
Alignment	THB.H12RSNP.2.SM.D.words.tsv
Threshold to P-value map	THB.H12RSNP.2.SM.D.thr
Motif in other formats
JASPAR format	THB.H12RSNP.2.SM.D_jaspar_format.txt
MEME format	THB.H12RSNP.2.SM.D_meme_format.meme
Transfac format	THB.H12RSNP.2.SM.D_transfac_format.txt
Homer format	THB.H12RSNP.2.SM.D_homer_format_0.001.txt THB.H12RSNP.2.SM.D_homer_format_0.0005.txt THB.H12RSNP.2.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	4296.75	694.75	4269.75	517.75
02	464.0	593.0	8242.0	480.0
03	326.0	464.0	8092.0	897.0
04	266.0	571.0	652.0	8290.0
05	379.0	8151.0	451.0	798.0
06	8999.0	202.0	329.0	249.0
07	8287.0	72.0	837.0	583.0
08	9223.0	8.0	547.0	1.0
09	2.0	4.0	9771.0	2.0
10	5.0	2.0	9423.0	349.0
11	6.0	31.0	341.0	9401.0
12	56.0	8547.0	213.0	963.0
13	8058.25	117.25	1487.25	116.25
14	2472.0	2549.0	1593.0	3165.0

PFM

	A	C	G	T
01	0.439	0.071	0.437	0.053
02	0.047	0.061	0.843	0.049
03	0.033	0.047	0.827	0.092
04	0.027	0.058	0.067	0.848
05	0.039	0.834	0.046	0.082
06	0.92	0.021	0.034	0.025
07	0.847	0.007	0.086	0.06
08	0.943	0.001	0.056	0.0
09	0.0	0.0	0.999	0.0
10	0.001	0.0	0.964	0.036
11	0.001	0.003	0.035	0.961
12	0.006	0.874	0.022	0.098
13	0.824	0.012	0.152	0.012
14	0.253	0.261	0.163	0.324

PWM

	A	C	G	T
01	0.564	-1.256	0.557	-1.549
02	-1.658	-1.414	1.215	-1.624
03	-2.009	-1.658	1.196	-1.001
04	-2.211	-1.451	-1.319	1.22
05	-1.859	1.204	-1.686	-1.118
06	1.302	-2.483	-2.0	-2.276
07	1.22	-3.495	-1.07	-1.431
08	1.327	-5.471	-1.494	-6.61
09	-6.345	-5.963	1.385	-6.345
10	-5.815	-6.345	1.349	-1.941
11	-5.687	-4.297	-1.964	1.346
12	-3.737	1.251	-2.431	-0.93
13	1.192	-3.019	-0.496	-3.027
14	0.011	0.042	-0.428	0.258

Standard thresholds

P-value	Threshold
0.001	1.42226
0.0005	2.82831
0.0001	5.69461