PRDM4.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRDM4.H12INVIVO.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	dRdbdGTTTChWKdnnhhYh
GC content	47.33%
Information content (bits; total / per base)	12.567 / 0.628
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)	0.882	0.926	0.822	0.878	0.877	0.931	4.243	5.122	209.0	231.31

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.958	0.958	0.827	0.847	0.671	0.716
Overall, 2 experiments	best	1.0	0.999	0.972	0.972	0.777	0.813
Methyl HT-SELEX, 1 experiments	median	1.0	0.999	0.972	0.972	0.777	0.813
Methyl HT-SELEX, 1 experiments	best	1.0	0.999	0.972	0.972	0.777	0.813
Non-Methyl HT-SELEX, 1 experiments	median	0.916	0.918	0.682	0.723	0.564	0.619
Non-Methyl HT-SELEX, 1 experiments	best	0.916	0.918	0.682	0.723	0.564	0.619

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.H12INVIVO.0.PSM.A.pcm
PWM	PRDM4.H12INVIVO.0.PSM.A.pwm
PFM	PRDM4.H12INVIVO.0.PSM.A.pfm
Alignment	PRDM4.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	PRDM4.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	PRDM4.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	PRDM4.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	PRDM4.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	PRDM4.H12INVIVO.0.PSM.A_homer_format_0.001.txt PRDM4.H12INVIVO.0.PSM.A_homer_format_0.0005.txt PRDM4.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	258.0	157.0	174.0	411.0
02	299.0	50.0	545.0	106.0
03	311.0	41.0	496.0	152.0
04	104.0	556.0	175.0	165.0
05	504.0	24.0	243.0	229.0
06	11.0	17.0	943.0	29.0
07	1.0	25.0	4.0	970.0
08	5.0	34.0	23.0	938.0
09	7.0	1.0	6.0	986.0
10	20.0	880.0	4.0	96.0
11	441.0	170.0	31.0	358.0
12	660.0	83.0	96.0	161.0
13	146.0	54.0	591.0	209.0
14	171.0	94.0	402.0	333.0
15	208.0	296.0	229.0	267.0
16	195.0	349.0	162.0	294.0
17	169.0	490.0	116.0	225.0
18	137.0	561.0	101.0	201.0
19	121.0	612.0	99.0	168.0
20	246.0	396.0	136.0	222.0

PFM

	A	C	G	T
01	0.258	0.157	0.174	0.411
02	0.299	0.05	0.545	0.106
03	0.311	0.041	0.496	0.152
04	0.104	0.556	0.175	0.165
05	0.504	0.024	0.243	0.229
06	0.011	0.017	0.943	0.029
07	0.001	0.025	0.004	0.97
08	0.005	0.034	0.023	0.938
09	0.007	0.001	0.006	0.986
10	0.02	0.88	0.004	0.096
11	0.441	0.17	0.031	0.358
12	0.66	0.083	0.096	0.161
13	0.146	0.054	0.591	0.209
14	0.171	0.094	0.402	0.333
15	0.208	0.296	0.229	0.267
16	0.195	0.349	0.162	0.294
17	0.169	0.49	0.116	0.225
18	0.137	0.561	0.101	0.201
19	0.121	0.612	0.099	0.168
20	0.246	0.396	0.136	0.222

PWM

	A	C	G	T
01	0.031	-0.461	-0.359	0.494
02	0.178	-1.582	0.776	-0.849
03	0.217	-1.774	0.682	-0.493
04	-0.867	0.796	-0.354	-0.412
05	0.698	-2.281	-0.028	-0.087
06	-2.985	-2.598	1.323	-2.103
07	-4.525	-2.243	-3.783	1.351
08	-3.622	-1.952	-2.32	1.317
09	-3.362	-4.525	-3.484	1.367
10	-2.45	1.254	-3.783	-0.946
11	0.565	-0.382	-2.04	0.357
12	0.967	-1.089	-0.946	-0.436
13	-0.533	-1.508	0.856	-0.178
14	-0.377	-0.967	0.472	0.285
15	-0.183	0.168	-0.087	0.065
16	-0.247	0.332	-0.43	0.161
17	-0.388	0.67	-0.76	-0.105
18	-0.596	0.804	-0.896	-0.216
19	-0.718	0.891	-0.916	-0.394
20	-0.016	0.457	-0.603	-0.118

Standard thresholds

P-value	Threshold
0.001	4.01746
0.0005	5.03086
0.0001	7.11406