RARA.H12RSNP.2.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RARA.H12RSNP.2.P.B
Gene (human)	RARA (GeneCards)
Gene synonyms (human)	NR1B1
Gene (mouse)	Rara
Gene synonyms (mouse)	Nr1b1
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	16
Consensus	vAGGTCAbnnhRhhYh
GC content	54.57%
Information content (bits; total / per base)	10.659 / 0.666
Data sources	ChIP-Seq
Aligned words	1001

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	5 (29)	0.714	0.814	0.525	0.779	0.667	0.771	1.604	3.383	47.959	135.699
Mouse	10 (46)	0.71	0.806	0.562	0.668	0.684	0.765	1.817	2.235	43.549	175.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.761	0.732	0.737	0.711	0.704	0.682
Overall, 4 experiments	best	0.952	0.919	0.934	0.897	0.886	0.849
Methyl HT-SELEX, 1 experiments	median	0.95	0.917	0.929	0.891	0.881	0.843
Methyl HT-SELEX, 1 experiments	best	0.95	0.917	0.929	0.891	0.881	0.843
Non-Methyl HT-SELEX, 3 experiments	median	0.572	0.547	0.544	0.531	0.527	0.521
Non-Methyl HT-SELEX, 3 experiments	best	0.952	0.919	0.934	0.897	0.886	0.849

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.56	1.639	0.152	0.053

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.559	0.077	0.417	0.207

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	RAR (NR1B) {2.1.2.1} (TFClass)
TFClass ID	TFClass: 2.1.2.1.1
HGNC	HGNC:9864
MGI	MGI:97856
EntrezGene (human)	GeneID:5914 (SSTAR profile)
EntrezGene (mouse)	GeneID:19401 (SSTAR profile)
UniProt ID (human)	RARA_HUMAN
UniProt ID (mouse)	RARA_MOUSE
UniProt AC (human)	P10276 (TFClass)
UniProt AC (mouse)	P11416 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 10 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	RARA.H12RSNP.2.P.B.pcm
PWM	RARA.H12RSNP.2.P.B.pwm
PFM	RARA.H12RSNP.2.P.B.pfm
Alignment	RARA.H12RSNP.2.P.B.words.tsv
Threshold to P-value map	RARA.H12RSNP.2.P.B.thr
Motif in other formats
JASPAR format	RARA.H12RSNP.2.P.B_jaspar_format.txt
MEME format	RARA.H12RSNP.2.P.B_meme_format.meme
Transfac format	RARA.H12RSNP.2.P.B_transfac_format.txt
Homer format	RARA.H12RSNP.2.P.B_homer_format_0.001.txt RARA.H12RSNP.2.P.B_homer_format_0.0005.txt RARA.H12RSNP.2.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	346.0	367.0	194.0	94.0
02	803.0	7.0	181.0	10.0
03	68.0	2.0	802.0	129.0
04	20.0	18.0	934.0	29.0
05	22.25	51.25	130.25	797.25
06	26.25	932.25	28.25	14.25
07	968.25	9.25	13.25	10.25
08	153.25	336.25	341.25	170.25
09	281.25	318.25	266.25	135.25
10	218.25	284.25	353.25	145.25
11	213.25	127.25	93.25	567.25
12	178.25	130.25	623.25	69.25
13	486.25	227.25	120.25	167.25
14	157.25	590.25	83.25	170.25
15	130.25	654.25	64.25	152.25
16	142.25	339.25	118.25	401.25

PFM

	A	C	G	T
01	0.346	0.367	0.194	0.094
02	0.802	0.007	0.181	0.01
03	0.068	0.002	0.801	0.129
04	0.02	0.018	0.933	0.029
05	0.022	0.051	0.13	0.796
06	0.026	0.931	0.028	0.014
07	0.967	0.009	0.013	0.01
08	0.153	0.336	0.341	0.17
09	0.281	0.318	0.266	0.135
10	0.218	0.284	0.353	0.145
11	0.213	0.127	0.093	0.567
12	0.178	0.13	0.623	0.069
13	0.486	0.227	0.12	0.167
14	0.157	0.59	0.083	0.17
15	0.13	0.654	0.064	0.152
16	0.142	0.339	0.118	0.401

PWM

	A	C	G	T
01	0.322	0.381	-0.253	-0.968
02	1.161	-3.363	-0.321	-3.067
03	-1.285	-4.214	1.16	-0.656
04	-2.451	-2.547	1.312	-2.104
05	-2.352	-1.559	-0.647	1.154
06	-2.198	1.31	-2.129	-2.758
07	1.348	-3.134	-2.823	-3.046
08	-0.486	0.294	0.308	-0.382
09	0.116	0.239	0.062	-0.61
10	-0.136	0.127	0.343	-0.539
11	-0.159	-0.67	-0.976	0.815
12	-0.337	-0.647	0.908	-1.267
13	0.661	-0.096	-0.726	-0.4
14	-0.461	0.854	-1.087	-0.382
15	-0.647	0.957	-1.34	-0.493
16	-0.56	0.302	-0.742	0.47

Standard thresholds

P-value	Threshold
0.001	4.57906
0.0005	5.45011
0.0001	7.23271