THB.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	THB.H12INVIVO.1.PSM.A
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	A

Motif length	10
Consensus	hRAGGWCAvv
GC content	55.71%
Information content (bits; total / per base)	10.611 / 1.061
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
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 (7)	0.769	0.784	0.536	0.551	0.808	0.815	2.424	2.442	151.013	165.509
Mouse	1 (5)	0.636	0.676	0.488	0.528	0.612	0.653	1.535	1.68	24.004	47.167

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.961	0.925	0.959	0.925	0.938	0.905
Overall, 6 experiments	best	0.99	0.982	0.987	0.978	0.975	0.963
Methyl HT-SELEX, 2 experiments	median	0.977	0.956	0.973	0.952	0.946	0.925
Methyl HT-SELEX, 2 experiments	best	0.99	0.982	0.987	0.977	0.966	0.953
Non-Methyl HT-SELEX, 4 experiments	median	0.829	0.806	0.771	0.761	0.741	0.734
Non-Methyl HT-SELEX, 4 experiments	best	0.99	0.982	0.987	0.978	0.975	0.963

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.H12INVIVO.1.PSM.A.pcm
PWM	THB.H12INVIVO.1.PSM.A.pwm
PFM	THB.H12INVIVO.1.PSM.A.pfm
Alignment	THB.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	THB.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	THB.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	THB.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	THB.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	THB.H12INVIVO.1.PSM.A_homer_format_0.001.txt THB.H12INVIVO.1.PSM.A_homer_format_0.0005.txt THB.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	157.0	244.0	66.0	533.0
02	282.0	133.0	576.0	9.0
03	787.0	2.0	210.0	1.0
04	23.0	1.0	971.0	5.0
05	6.0	5.0	968.0	21.0
06	225.0	44.0	23.0	708.0
07	2.0	991.0	5.0	2.0
08	985.0	3.0	5.0	7.0
09	141.0	245.0	481.0	133.0
10	266.0	211.0	387.0	136.0

PFM

	A	C	G	T
01	0.157	0.244	0.066	0.533
02	0.282	0.133	0.576	0.009
03	0.787	0.002	0.21	0.001
04	0.023	0.001	0.971	0.005
05	0.006	0.005	0.968	0.021
06	0.225	0.044	0.023	0.708
07	0.002	0.991	0.005	0.002
08	0.985	0.003	0.005	0.007
09	0.141	0.245	0.481	0.133
10	0.266	0.211	0.387	0.136

PWM

	A	C	G	T
01	-0.461	-0.024	-1.313	0.753
02	0.12	-0.625	0.831	-3.156
03	1.142	-4.213	-0.173	-4.525
04	-2.32	-4.525	1.352	-3.622
05	-3.484	-3.622	1.349	-2.405
06	-0.105	-1.706	-2.32	1.037
07	-4.213	1.372	-3.622	-4.213
08	1.366	-3.975	-3.622	-3.362
09	-0.567	-0.02	0.651	-0.625
10	0.062	-0.168	0.435	-0.603

Standard thresholds

P-value	Threshold
0.001	4.44701
0.0005	5.65022
0.0001	7.68537