PRDM1.H13RSNP.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRDM1.H13RSNP.1.PS.A
Gene (human)	PRDM1 (GeneCards)
Gene synonyms (human)	BLIMP1
Gene (mouse)	Prdm1
Gene synonyms (mouse)	Blimp1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	15
Consensus	RRAAGdGAAAGKRRd
GC content	41.88%
Information content (bits; total / per base)	17.584 / 1.172
Data sources	ChIP-Seq + HT-SELEX
Aligned words	992
Previous names	PRDM1.H12RSNP.1.PS.A

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	6 (35)	0.852	0.946	0.785	0.905	0.87	0.95	3.939	5.196	173.638	417.409
Mouse	13 (72)	0.876	0.956	0.79	0.902	0.898	0.974	4.982	7.783	132.714	626.041

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.833	0.826	0.727	0.724	0.638	0.647
Overall, 4 experiments	best	0.975	0.963	0.93	0.91	0.81	0.806
Methyl HT-SELEX, 1 experiments	median	0.975	0.963	0.93	0.91	0.81	0.806
Methyl HT-SELEX, 1 experiments	best	0.975	0.963	0.93	0.91	0.81	0.806
Non-Methyl HT-SELEX, 3 experiments	median	0.733	0.747	0.602	0.626	0.549	0.572
Non-Methyl HT-SELEX, 3 experiments	best	0.934	0.905	0.852	0.822	0.726	0.722

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.683	4.85	0.139	0.114

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.959	0.839	0.784	0.685

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	PRDM1-like {2.3.3.12} (TFClass)
TFClass ID	TFClass: 2.3.3.12.1
HGNC	HGNC:9346
MGI	MGI:99655
EntrezGene (human)	GeneID:639 (SSTAR profile)
EntrezGene (mouse)	GeneID:12142 (SSTAR profile)
UniProt ID (human)	PRDM1_HUMAN
UniProt ID (mouse)	PRDM1_MOUSE
UniProt AC (human)	O75626 (TFClass)
UniProt AC (mouse)	Q60636 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	6 human, 13 mouse
HT-SELEX	3
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	PRDM1.H13RSNP.1.PS.A.pcm
PWM	PRDM1.H13RSNP.1.PS.A.pwm
PFM	PRDM1.H13RSNP.1.PS.A.pfm
Threshold to P-value map	PRDM1.H13RSNP.1.PS.A.thr
Motif in other formats
JASPAR format	PRDM1.H13RSNP.1.PS.A_jaspar_format.txt
MEME format	PRDM1.H13RSNP.1.PS.A_meme_format.meme
Transfac format	PRDM1.H13RSNP.1.PS.A_transfac_format.txt
Homer format	PRDM1.H13RSNP.1.PS.A_homer_format_0.001.txt PRDM1.H13RSNP.1.PS.A_homer_format_0.0005.txt PRDM1.H13RSNP.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	216.0	26.0	717.0	33.0
02	791.0	52.0	111.0	38.0
03	857.0	52.0	57.0	26.0
04	928.0	2.0	59.0	3.0
05	32.0	19.0	930.0	11.0
06	113.0	55.0	459.0	365.0
07	30.0	3.0	957.0	2.0
08	984.0	0.0	3.0	5.0
09	952.0	5.0	33.0	2.0
10	974.0	1.0	14.0	3.0
11	22.0	19.0	944.0	7.0
12	28.0	69.0	374.0	521.0
13	190.0	58.0	664.0	80.0
14	632.0	100.0	184.0	76.0
15	557.0	116.0	148.0	171.0

PFM

	A	C	G	T
01	0.218	0.026	0.723	0.033
02	0.797	0.052	0.112	0.038
03	0.864	0.052	0.057	0.026
04	0.935	0.002	0.059	0.003
05	0.032	0.019	0.938	0.011
06	0.114	0.055	0.463	0.368
07	0.03	0.003	0.965	0.002
08	0.992	0.0	0.003	0.005
09	0.96	0.005	0.033	0.002
10	0.982	0.001	0.014	0.003
11	0.022	0.019	0.952	0.007
12	0.028	0.07	0.377	0.525
13	0.192	0.058	0.669	0.081
14	0.637	0.101	0.185	0.077
15	0.561	0.117	0.149	0.172

PWM

	A	C	G	T
01	-0.137	-2.198	1.057	-1.973
02	1.155	-1.536	-0.795	-1.838
03	1.235	-1.536	-1.447	-2.198
04	1.315	-4.205	-1.414	-3.968
05	-2.002	-2.489	1.317	-2.977
06	-0.778	-1.482	0.612	0.384
07	-2.063	-3.968	1.345	-4.205
08	1.373	-4.975	-3.968	-3.615
09	1.34	-3.615	-1.973	-4.205
10	1.363	-4.518	-2.765	-3.968
11	-2.354	-2.489	1.332	-3.354
12	-2.128	-1.262	0.408	0.739
13	-0.264	-1.431	0.981	-1.117
14	0.931	-0.898	-0.296	-1.167
15	0.805	-0.752	-0.512	-0.369

Standard thresholds

P-value	Threshold
0.001	1.61881
0.0005	2.94016
0.0001	5.71766