PRDM4.H12CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRDM4.H12CORE.0.PSM.A
Gene (human)	PRDM4 (GeneCards)
Gene synonyms (human)	PFM1
Gene (mouse)	Prdm4
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	20
Consensus	dRRbRGTTTChWKdnnhYYh
GC content	48.5%
Information content (bits; total / per base)	13.906 / 0.695
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	304

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)	0.882	0.933	0.823	0.886	0.869	0.93	4.236	5.22	207.854	223.569

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.959	0.96	0.831	0.851	0.675	0.719
Overall, 2 experiments	best	1.0	1.0	0.975	0.975	0.78	0.815
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.975	0.975	0.78	0.815
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.975	0.975	0.78	0.815
Non-Methyl HT-SELEX, 1 experiments	median	0.919	0.921	0.687	0.727	0.57	0.622
Non-Methyl HT-SELEX, 1 experiments	best	0.919	0.921	0.687	0.727	0.57	0.622

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	Multiple dispersed zinc fingers {2.3.4} (TFClass)
TF subfamily	Unclassified {2.3.4.0} (TFClass)
TFClass ID	TFClass: 2.3.4.0.31
HGNC	HGNC:9348
MGI	MGI:1920093
EntrezGene (human)	GeneID:11108 (SSTAR profile)
EntrezGene (mouse)	GeneID:72843 (SSTAR profile)
UniProt ID (human)	PRDM4_HUMAN
UniProt ID (mouse)	PRDM4_MOUSE
UniProt AC (human)	Q9UKN5 (TFClass)
UniProt AC (mouse)	Q80V63 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	PRDM4.H12CORE.0.PSM.A.pcm
PWM	PRDM4.H12CORE.0.PSM.A.pwm
PFM	PRDM4.H12CORE.0.PSM.A.pfm
Alignment	PRDM4.H12CORE.0.PSM.A.words.tsv
Threshold to P-value map	PRDM4.H12CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	PRDM4.H12CORE.0.PSM.A_jaspar_format.txt
MEME format	PRDM4.H12CORE.0.PSM.A_meme_format.meme
Transfac format	PRDM4.H12CORE.0.PSM.A_transfac_format.txt
Homer format	PRDM4.H12CORE.0.PSM.A_homer_format_0.001.txt PRDM4.H12CORE.0.PSM.A_homer_format_0.0005.txt PRDM4.H12CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	64.0	57.0	58.0	125.0
02	90.0	14.0	165.0	35.0
03	93.0	7.0	175.0	29.0
04	30.0	172.0	45.0	57.0
05	168.0	8.0	66.0	62.0
06	3.0	1.0	291.0	9.0
07	1.0	6.0	0.0	297.0
08	1.0	6.0	8.0	289.0
09	2.0	1.0	1.0	300.0
10	8.0	267.0	0.0	29.0
11	149.0	48.0	14.0	93.0
12	228.0	18.0	17.0	41.0
13	32.0	15.0	206.0	51.0
14	53.0	26.0	146.0	79.0
15	75.0	92.0	67.0	70.0
16	68.0	105.0	43.0	88.0
17	51.0	155.0	37.0	61.0
18	38.0	190.0	24.0	52.0
19	27.0	202.0	28.0	47.0
20	72.0	137.0	31.0	64.0

PFM

	A	C	G	T
01	0.211	0.188	0.191	0.411
02	0.296	0.046	0.543	0.115
03	0.306	0.023	0.576	0.095
04	0.099	0.566	0.148	0.188
05	0.553	0.026	0.217	0.204
06	0.01	0.003	0.957	0.03
07	0.003	0.02	0.0	0.977
08	0.003	0.02	0.026	0.951
09	0.007	0.003	0.003	0.987
10	0.026	0.878	0.0	0.095
11	0.49	0.158	0.046	0.306
12	0.75	0.059	0.056	0.135
13	0.105	0.049	0.678	0.168
14	0.174	0.086	0.48	0.26
15	0.247	0.303	0.22	0.23
16	0.224	0.345	0.141	0.289
17	0.168	0.51	0.122	0.201
18	0.125	0.625	0.079	0.171
19	0.089	0.664	0.092	0.155
20	0.237	0.451	0.102	0.211

PWM

	A	C	G	T
01	-0.168	-0.282	-0.265	0.49
02	0.166	-1.613	0.765	-0.754
03	0.198	-2.218	0.824	-0.934
04	-0.902	0.806	-0.511	-0.282
05	0.783	-2.106	-0.138	-0.199
06	-2.861	-3.462	1.329	-2.005
07	-3.462	-2.344	-3.992	1.349
08	-3.462	-2.344	-2.106	1.322
09	-3.117	-3.462	-3.462	1.359
10	-2.106	1.243	-3.992	-0.934
11	0.664	-0.449	-1.613	0.198
12	1.086	-1.383	-1.435	-0.602
13	-0.84	-1.55	0.985	-0.39
14	-0.352	-1.038	0.644	0.038
15	-0.013	0.188	-0.124	-0.081
16	-0.109	0.318	-0.555	0.144
17	-0.39	0.703	-0.701	-0.215
18	-0.675	0.905	-1.113	-0.371
19	-1.002	0.966	-0.967	-0.469
20	-0.053	0.581	-0.87	-0.168

Standard thresholds

P-value	Threshold
0.001	3.73186
0.0005	4.77136
0.0001	6.93151