PRDM13.H13INVIVO.0.PSGI.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRDM13.H13INVIVO.0.PSGI.A
Gene (human)	PRDM13 (GeneCards)
Gene synonyms (human)	PFM10
Gene (mouse)	Prdm13
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	10
Consensus	dGCWGGTGbb
GC content	69.01%
Information content (bits; total / per base)	11.436 / 1.144
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX + SMiLe-Seq
Aligned words	1000
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 (2)	0.852	0.859	0.708	0.712	0.766	0.778	142.266	145.678

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
overall, 5 experiments	median	0.984	0.978	0.936	0.918	0.808	0.807
overall, 5 experiments	best	0.999	0.999	0.999	0.998	0.996	0.995
Lysate, 2 experiments	median	0.961	0.949	0.884	0.867	0.751	0.756
Lysate, 2 experiments	best	0.979	0.971	0.936	0.918	0.808	0.807
IVT, 1 experiments	median	0.984	0.978	0.89	0.884	0.726	0.749
IVT, 1 experiments	best	0.984	0.978	0.89	0.884	0.726	0.749
GFPIVT, 2 experiments	median	0.994	0.992	0.981	0.974	0.916	0.918
GFPIVT, 2 experiments	best	0.999	0.999	0.999	0.998	0.996	0.995

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
overall, 5 experiments	median	189.563	0.863	0.934	0.851
overall, 5 experiments	best	489.854	0.945	0.963	0.896
Lysate, 2 experiments	median	451.122	0.867	0.938	0.853
Lysate, 2 experiments	best	458.244	0.875	0.939	0.853
IVT, 1 experiments	median	158.523	0.863	0.93	0.851
IVT, 1 experiments	best	158.523	0.863	0.93	0.851
GFPIVT, 2 experiments	median	134.367	0.862	0.919	0.804
GFPIVT, 2 experiments	best	489.854	0.945	0.963	0.896

SMiLE-Seq benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 1 experiments	median	0.934	0.896	0.883	0.844	0.749	0.742
Overall, 1 experiments	best	0.934	0.896	0.883	0.844	0.749	0.742

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: 2.3.4.0.12
HGNC	HGNC:13998
MGI	MGI:2448528
EntrezGene (human)	GeneID:59336 (SSTAR profile)
EntrezGene (mouse)	GeneID:230025 (SSTAR profile)
UniProt ID (human)	PRD13_HUMAN
UniProt ID (mouse)	PRD13_MOUSE
UniProt AC (human)	Q9H4Q3 (TFClass)
UniProt AC (mouse)	E9PZZ1 (TFClass)
GRECO-DB-TF	no

ChIP-Seq	2 human, 0 mouse
HT-SELEX	5 overall: 2 Lysate, 1 IVT, 2 GFPIVT
Genomic HT-SELEX	5 overall: 2 Lysate, 1 IVT, 2 GFPIVT
SMiLE-Seq	1
PBM	0

PCM	PRDM13.H13INVIVO.0.PSGI.A.pcm
PWM	PRDM13.H13INVIVO.0.PSGI.A.pwm
PFM	PRDM13.H13INVIVO.0.PSGI.A.pfm
Threshold to P-value map	PRDM13.H13INVIVO.0.PSGI.A.thr
Motif in other formats
JASPAR format	PRDM13.H13INVIVO.0.PSGI.A_jaspar_format.txt
MEME format	PRDM13.H13INVIVO.0.PSGI.A_meme_format.meme
Transfac format	PRDM13.H13INVIVO.0.PSGI.A_transfac_format.txt
Homer format	PRDM13.H13INVIVO.0.PSGI.A_homer_format_0.001.txt PRDM13.H13INVIVO.0.PSGI.A_homer_format_0.0005.txt PRDM13.H13INVIVO.0.PSGI.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	315.0	71.0	379.0	235.0
02	77.0	25.0	891.0	7.0
03	8.0	970.0	7.0	15.0
04	492.0	10.0	104.0	394.0
05	3.0	1.0	995.0	1.0
06	4.0	7.0	989.0	0.0
07	6.0	1.0	1.0	992.0
08	83.0	35.0	835.0	47.0
09	61.0	287.0	538.0	114.0
10	86.0	496.0	259.0	159.0

PFM

	A	C	G	T
01	0.315	0.071	0.379	0.235
02	0.077	0.025	0.891	0.007
03	0.008	0.97	0.007	0.015
04	0.492	0.01	0.104	0.394
05	0.003	0.001	0.995	0.001
06	0.004	0.007	0.989	0.0
07	0.006	0.001	0.001	0.992
08	0.083	0.035	0.835	0.047
09	0.061	0.287	0.538	0.114
10	0.086	0.496	0.259	0.159

PWM

	A	C	G	T
01	0.23	-1.242	0.414	-0.061
02	-1.162	-2.243	1.266	-3.362
03	-3.253	1.351	-3.362	-2.711
04	0.674	-3.066	-0.867	0.452
05	-3.975	-4.525	1.376	-4.525
06	-3.783	-3.362	1.37	-4.982
07	-3.484	-4.525	-4.525	1.373
08	-1.089	-1.925	1.201	-1.642
09	-1.39	0.137	0.763	-0.777
10	-1.054	0.682	0.035	-0.449

Standard thresholds

P-value	Threshold
0.001	4.225265
0.0005	5.29946
0.0001	7.468375