THB.H12RSNP.1.PSM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	THB.H12RSNP.1.PSM.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	1
Quality	D

Motif length	9
Consensus	vhvRGRdCA
GC content	53.9%
Information content (bits; total / per base)	7.13 / 0.792
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	996

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)	0.795	0.809	0.622	0.642	0.793	0.795	2.294	2.311	134.051	154.585
Mouse	1 (5)	0.643	0.677	0.494	0.531	0.599	0.64	1.478	1.64	17.585	33.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.985	0.973	0.976	0.962	0.947	0.929
Overall, 6 experiments	best	0.991	0.984	0.987	0.977	0.972	0.959
Methyl HT-SELEX, 2 experiments	median	0.985	0.975	0.976	0.962	0.947	0.929
Methyl HT-SELEX, 2 experiments	best	0.991	0.984	0.985	0.976	0.964	0.951
Non-Methyl HT-SELEX, 4 experiments	median	0.844	0.833	0.787	0.787	0.757	0.757
Non-Methyl HT-SELEX, 4 experiments	best	0.99	0.983	0.987	0.977	0.972	0.959

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.1.PSM.D.pcm
PWM	THB.H12RSNP.1.PSM.D.pwm
PFM	THB.H12RSNP.1.PSM.D.pfm
Alignment	THB.H12RSNP.1.PSM.D.words.tsv
Threshold to P-value map	THB.H12RSNP.1.PSM.D.thr
Motif in other formats
JASPAR format	THB.H12RSNP.1.PSM.D_jaspar_format.txt
MEME format	THB.H12RSNP.1.PSM.D_meme_format.meme
Transfac format	THB.H12RSNP.1.PSM.D_transfac_format.txt
Homer format	THB.H12RSNP.1.PSM.D_homer_format_0.001.txt THB.H12RSNP.1.PSM.D_homer_format_0.0005.txt THB.H12RSNP.1.PSM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	164.0	458.0	247.0	127.0
02	281.0	214.0	82.0	419.0
03	299.0	182.0	492.0	23.0
04	714.0	1.0	242.0	39.0
05	22.0	1.0	939.0	34.0
06	106.0	29.0	782.0	79.0
07	256.0	106.0	131.0	503.0
08	59.0	820.0	73.0	44.0
09	921.0	12.0	21.0	42.0

PFM

	A	C	G	T
01	0.165	0.46	0.248	0.128
02	0.282	0.215	0.082	0.421
03	0.3	0.183	0.494	0.023
04	0.717	0.001	0.243	0.039
05	0.022	0.001	0.943	0.034
06	0.106	0.029	0.785	0.079
07	0.257	0.106	0.132	0.505
08	0.059	0.823	0.073	0.044
09	0.925	0.012	0.021	0.042

PWM

	A	C	G	T
01	-0.414	0.606	-0.008	-0.667
02	0.12	-0.15	-1.097	0.518
03	0.182	-0.311	0.678	-2.317
04	1.049	-4.522	-0.028	-1.817
05	-2.358	-4.522	1.322	-1.948
06	-0.845	-2.099	1.14	-1.133
07	0.028	-0.845	-0.636	0.7
08	-1.418	1.187	-1.211	-1.702
09	1.303	-2.905	-2.401	-1.746

Standard thresholds

P-value	Threshold
0.001	5.097415
0.0005	5.771545
0.0001	6.934685