THB.H12INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	THB.H12INVITRO.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	nYRAGGTCAn
GC content	43.95%
Information content (bits; total / per base)	11.92 / 1.192
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	2433

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)	0.743	0.763	0.551	0.578	0.741	0.753	2.001	2.05	133.066	146.26
Mouse	1 (5)	0.615	0.619	0.45	0.469	0.56	0.571	1.291	1.341	14.398	27.444

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.975	0.953	0.968	0.946	0.941	0.916
Overall, 6 experiments	best	0.996	0.993	0.992	0.987	0.98	0.972
Methyl HT-SELEX, 2 experiments	median	0.985	0.972	0.977	0.963	0.951	0.933
Methyl HT-SELEX, 2 experiments	best	0.996	0.993	0.992	0.987	0.977	0.969
Non-Methyl HT-SELEX, 4 experiments	median	0.842	0.832	0.781	0.78	0.749	0.748
Non-Methyl HT-SELEX, 4 experiments	best	0.995	0.992	0.992	0.987	0.98	0.972

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.H12INVITRO.1.PSM.A.pcm
PWM	THB.H12INVITRO.1.PSM.A.pwm
PFM	THB.H12INVITRO.1.PSM.A.pfm
Alignment	THB.H12INVITRO.1.PSM.A.words.tsv
Threshold to P-value map	THB.H12INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	THB.H12INVITRO.1.PSM.A_jaspar_format.txt
MEME format	THB.H12INVITRO.1.PSM.A_meme_format.meme
Transfac format	THB.H12INVITRO.1.PSM.A_transfac_format.txt
Homer format	THB.H12INVITRO.1.PSM.A_homer_format_0.001.txt THB.H12INVITRO.1.PSM.A_homer_format_0.0005.txt THB.H12INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	906.5	359.5	576.5	590.5
02	140.75	270.75	136.75	1884.75
03	1517.0	251.0	597.0	68.0
04	2401.0	3.0	20.0	9.0
05	0.0	0.0	2433.0	0.0
06	0.0	0.0	2433.0	0.0
07	126.0	2.0	51.0	2254.0
08	88.0	2206.0	97.0	42.0
09	2225.0	54.0	117.0	37.0
10	613.5	741.5	343.5	734.5

PFM

	A	C	G	T
01	0.373	0.148	0.237	0.243
02	0.058	0.111	0.056	0.775
03	0.624	0.103	0.245	0.028
04	0.987	0.001	0.008	0.004
05	0.0	0.0	1.0	0.0
06	0.0	0.0	1.0	0.0
07	0.052	0.001	0.021	0.926
08	0.036	0.907	0.04	0.017
09	0.915	0.022	0.048	0.015
10	0.252	0.305	0.141	0.302

PWM

	A	C	G	T
01	0.398	-0.524	-0.053	-0.03
02	-1.453	-0.805	-1.481	1.129
03	0.912	-0.881	-0.019	-2.166
04	1.371	-4.815	-3.325	-4.021
05	-5.746	-5.746	1.384	-5.746
06	-5.746	-5.746	1.384	-5.746
07	-1.562	-5.04	-2.444	1.308
08	-1.915	1.286	-1.819	-2.631
09	1.295	-2.389	-1.635	-2.752
10	0.009	0.198	-0.569	0.188

Standard thresholds

P-value	Threshold
0.001	3.96276
0.0005	5.090845
0.0001	7.32498