PRDM5.H13RSNP.0.PSGI.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRDM5.H13RSNP.0.PSGI.D
Gene (human)	PRDM5 (GeneCards)
Gene synonyms (human)	PFM2
Gene (mouse)	Prdm5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	26
Consensus	nMMCYbRWbCWCCdYnhRnnCChKdn
GC content	58.24%
Information content (bits; total / per base)	16.433 / 0.632
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX + SMiLe-Seq
Aligned words	2325
Previous names

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	Centrality, median	Centrality, best
Overall	2 (3)	0.816	0.851	0.691	0.762	0.723	0.749	97.201	136.509

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
overall, 4 experiments	median	0.997	0.996	0.958	0.956	0.863	0.878
overall, 4 experiments	best	1.0	0.999	0.999	0.998	0.995	0.993
Lysate, 2 experiments	median	0.99	0.986	0.89	0.889	0.716	0.746
Lysate, 2 experiments	best	0.995	0.993	0.917	0.915	0.733	0.765
GFPIVT, 2 experiments	median	1.0	0.999	0.999	0.998	0.994	0.992
GFPIVT, 2 experiments	best	1.0	0.999	0.999	0.998	0.995	0.993

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
overall, 4 experiments	median	335.825	0.886	0.878	0.778
overall, 4 experiments	best	516.409	0.903	0.889	0.82
Lysate, 2 experiments	median	319.878	0.851	0.834	0.733
Lysate, 2 experiments	best	392.796	0.884	0.881	0.78
GFPIVT, 2 experiments	median	353.484	0.893	0.878	0.79
GFPIVT, 2 experiments	best	516.409	0.903	0.889	0.82

SMiLE-Seq benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.852	0.843	0.724	0.736	0.628	0.651
Overall, 2 experiments	best	0.97	0.958	0.888	0.872	0.745	0.752

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	More than 3 adjacent zinc fingers {2.3.3} (TFClass)
TF subfamily	Unclassified {2.3.3.0} (TFClass)
TFClass ID	TFClass: 2.3.3.0.195
HGNC	HGNC:9349
MGI	MGI:1918029
EntrezGene (human)	GeneID:11107 (SSTAR profile)
EntrezGene (mouse)	GeneID:70779 (SSTAR profile)
UniProt ID (human)	PRDM5_HUMAN
UniProt ID (mouse)	PRDM5_MOUSE
UniProt AC (human)	Q9NQX1 (TFClass)
UniProt AC (mouse)	Q9CXE0 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 0 mouse
HT-SELEX	4 overall: 2 Lysate, 0 IVT, 2 GFPIVT
Genomic HT-SELEX	4 overall: 2 Lysate, 0 IVT, 2 GFPIVT
SMiLE-Seq	2
PBM	0

PCM	PRDM5.H13RSNP.0.PSGI.D.pcm
PWM	PRDM5.H13RSNP.0.PSGI.D.pwm
PFM	PRDM5.H13RSNP.0.PSGI.D.pfm
Threshold to P-value map	PRDM5.H13RSNP.0.PSGI.D.thr
Motif in other formats
JASPAR format	PRDM5.H13RSNP.0.PSGI.D_jaspar_format.txt
MEME format	PRDM5.H13RSNP.0.PSGI.D_meme_format.meme
Transfac format	PRDM5.H13RSNP.0.PSGI.D_transfac_format.txt
Homer format	PRDM5.H13RSNP.0.PSGI.D_homer_format_0.001.txt PRDM5.H13RSNP.0.PSGI.D_homer_format_0.0005.txt PRDM5.H13RSNP.0.PSGI.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	682.75	571.75	489.75	580.75
02	1441.0	331.0	259.0	294.0
03	1003.0	1156.0	102.0	64.0
04	53.0	2224.0	16.0	32.0
05	188.0	1327.0	55.0	755.0
06	112.0	498.0	474.0	1241.0
07	535.0	146.0	1454.0	190.0
08	1382.0	389.0	109.0	445.0
09	68.0	768.0	412.0	1077.0
10	68.0	2126.0	8.0	123.0
11	1205.0	25.0	43.0	1052.0
12	1.0	2324.0	0.0	0.0
13	0.0	2325.0	0.0	0.0
14	718.0	175.0	933.0	499.0
15	52.0	638.0	353.0	1282.0
16	287.0	686.0	584.0	768.0
17	462.0	1267.0	271.0	325.0
18	447.0	173.0	1466.0	239.0
19	721.0	564.0	645.0	395.0
20	699.0	588.0	632.0	406.0
21	100.0	2045.0	77.0	103.0
22	138.0	1892.0	127.0	168.0
23	192.0	879.0	189.0	1065.0
24	233.0	178.0	540.0	1374.0
25	261.5	232.5	1161.5	669.5
26	618.0	474.0	802.0	431.0

PFM

	A	C	G	T
01	0.294	0.246	0.211	0.25
02	0.62	0.142	0.111	0.126
03	0.431	0.497	0.044	0.028
04	0.023	0.957	0.007	0.014
05	0.081	0.571	0.024	0.325
06	0.048	0.214	0.204	0.534
07	0.23	0.063	0.625	0.082
08	0.594	0.167	0.047	0.191
09	0.029	0.33	0.177	0.463
10	0.029	0.914	0.003	0.053
11	0.518	0.011	0.018	0.452
12	0.0	1.0	0.0	0.0
13	0.0	1.0	0.0	0.0
14	0.309	0.075	0.401	0.215
15	0.022	0.274	0.152	0.551
16	0.123	0.295	0.251	0.33
17	0.199	0.545	0.117	0.14
18	0.192	0.074	0.631	0.103
19	0.31	0.243	0.277	0.17
20	0.301	0.253	0.272	0.175
21	0.043	0.88	0.033	0.044
22	0.059	0.814	0.055	0.072
23	0.083	0.378	0.081	0.458
24	0.1	0.077	0.232	0.591
25	0.112	0.1	0.5	0.288
26	0.266	0.204	0.345	0.185

PWM

	A	C	G	T
01	0.16	-0.016	-0.171	-0.001
02	0.906	-0.561	-0.804	-0.678
03	0.544	0.686	-1.725	-2.18
04	-2.362	1.339	-3.482	-2.844
05	-1.122	0.824	-2.327	0.261
06	-1.633	-0.154	-0.203	0.757
07	-0.083	-1.372	0.915	-1.111
08	0.864	-0.4	-1.66	-0.266
09	-2.121	0.278	-0.343	0.615
10	-2.121	1.294	-4.072	-1.541
11	0.727	-3.075	-2.563	0.592
12	-5.291	1.383	-5.707	-5.707
13	-5.707	1.384	-5.707	-5.707
14	0.211	-1.193	0.472	-0.152
15	-2.381	0.093	-0.497	0.789
16	-0.702	0.165	0.005	0.278
17	-0.229	0.777	-0.759	-0.579
18	-0.262	-1.204	0.923	-0.884
19	0.215	-0.03	0.104	-0.385
20	0.184	0.012	0.083	-0.357
21	-1.744	1.256	-2.0	-1.715
22	-1.427	1.178	-1.509	-1.233
23	-1.101	0.412	-1.117	0.604
24	-0.909	-1.176	-0.073	0.858
25	-0.795	-0.911	0.691	0.141
26	0.061	-0.203	0.321	-0.298

Standard thresholds

P-value	Threshold
0.001	2.31801
0.0005	3.59126
0.0001	6.20596