PRDM4.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRDM4.H12INVITRO.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	14
Consensus	dRCRGTTTCRAGdn
GC content	49.61%
Information content (bits; total / per base)	17.214 / 1.23
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8336

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)	0.842	0.892	0.764	0.822	0.825	0.874	3.237	3.787	166.509	194.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.953	0.948	0.849	0.859	0.719	0.748
Overall, 2 experiments	best	0.999	0.999	0.992	0.99	0.849	0.868
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.992	0.99	0.849	0.868
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.992	0.99	0.849	0.868
Non-Methyl HT-SELEX, 1 experiments	median	0.906	0.897	0.706	0.728	0.589	0.628
Non-Methyl HT-SELEX, 1 experiments	best	0.906	0.897	0.706	0.728	0.589	0.628

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.H12INVITRO.0.PSM.A.pcm
PWM	PRDM4.H12INVITRO.0.PSM.A.pwm
PFM	PRDM4.H12INVITRO.0.PSM.A.pfm
Alignment	PRDM4.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	PRDM4.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	PRDM4.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	PRDM4.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	PRDM4.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	PRDM4.H12INVITRO.0.PSM.A_homer_format_0.001.txt PRDM4.H12INVITRO.0.PSM.A_homer_format_0.0005.txt PRDM4.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3608.25	481.25	3472.25	774.25
02	2729.0	294.0	4866.0	447.0
03	174.0	7601.0	166.0	395.0
04	4255.0	19.0	2706.0	1356.0
05	0.0	0.0	8336.0	0.0
06	0.0	0.0	0.0	8336.0
07	0.0	1.0	0.0	8335.0
08	0.0	0.0	0.0	8336.0
09	0.0	8331.0	0.0	5.0
10	3275.0	24.0	4418.0	619.0
11	8129.0	41.0	38.0	128.0
12	365.0	109.0	7508.0	354.0
13	1120.25	541.25	4159.25	2515.25
14	1727.5	1985.5	2795.5	1827.5

PFM

	A	C	G	T
01	0.433	0.058	0.417	0.093
02	0.327	0.035	0.584	0.054
03	0.021	0.912	0.02	0.047
04	0.51	0.002	0.325	0.163
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.0	0.999	0.0	0.001
10	0.393	0.003	0.53	0.074
11	0.975	0.005	0.005	0.015
12	0.044	0.013	0.901	0.042
13	0.134	0.065	0.499	0.302
14	0.207	0.238	0.335	0.219

PWM

	A	C	G	T
01	0.548	-1.462	0.51	-0.988
02	0.269	-1.952	0.847	-1.536
03	-2.471	1.293	-2.518	-1.659
04	0.713	-4.586	0.261	-0.429
05	-6.829	-6.829	1.385	-6.829
06	-6.829	-6.829	-6.829	1.385
07	-6.829	-6.462	-6.829	1.385
08	-6.829	-6.829	-6.829	1.385
09	-6.829	1.385	-6.829	-5.661
10	0.452	-4.375	0.751	-1.211
11	1.36	-3.876	-3.948	-2.774
12	-1.737	-2.931	1.281	-1.767
13	-0.62	-1.345	0.691	0.188
14	-0.187	-0.048	0.293	-0.131

Standard thresholds

P-value	Threshold
0.001	-1.14269
0.0005	0.74821
0.0001	4.73991