PRDM1.H14INVIVO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PRDM1.H14INVIVO.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	14
Consensus	vRRAGdGAAAGTdv
GC content	40.01%
Information content (bits; total / per base)	14.24 / 1.017
Data sources	ChIP-Seq + HT-SELEX
Aligned words	980
Previous names	PRDM1.H12INVIVO.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)	0.911	0.983	0.864	0.969	0.913	0.975	4.55	5.886	238.215	587.229
Mouse	13 (72)	0.917	0.98	0.867	0.959	0.936	0.985	4.925	6.17	171.472	670.292

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.848	0.847	0.746	0.748	0.649	0.663
Overall, 4 experiments	best	0.989	0.983	0.966	0.954	0.85	0.851
Methyl HT-SELEX, 1 experiments	median	0.989	0.983	0.966	0.954	0.85	0.851
Methyl HT-SELEX, 1 experiments	best	0.989	0.983	0.966	0.954	0.85	0.851
Non-Methyl HT-SELEX, 3 experiments	median	0.739	0.758	0.603	0.631	0.548	0.573
Non-Methyl HT-SELEX, 3 experiments	best	0.958	0.937	0.89	0.865	0.751	0.753

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.891	4.934	0.162	0.133

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.801	0.628	0.756	0.641

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.H14INVIVO.1.PS.A.pcm
PWM	PRDM1.H14INVIVO.1.PS.A.pwm
PFM	PRDM1.H14INVIVO.1.PS.A.pfm
Threshold to P-value map	PRDM1.H14INVIVO.1.PS.A.thr
Motif in other formats
JASPAR format	PRDM1.H14INVIVO.1.PS.A_jaspar_format.txt
MEME format	PRDM1.H14INVIVO.1.PS.A_meme_format.meme
Transfac format	PRDM1.H14INVIVO.1.PS.A_transfac_format.txt
Homer format	PRDM1.H14INVIVO.1.PS.A_homer_format_0.001.txt PRDM1.H14INVIVO.1.PS.A_homer_format_0.0005.txt PRDM1.H14INVIVO.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	330.0	98.0	474.0	78.0
02	617.0	125.0	150.0	88.0
03	684.0	92.0	119.0	85.0
04	831.0	5.0	123.0	21.0
05	71.0	51.0	817.0	41.0
06	217.0	71.0	152.0	540.0
07	36.0	1.0	943.0	0.0
08	958.0	12.0	5.0	5.0
09	890.0	6.0	82.0	2.0
10	958.0	2.0	16.0	4.0
11	47.0	10.0	918.0	5.0
12	6.0	80.0	72.0	822.0
13	131.0	128.0	542.0	179.0
14	404.0	187.0	208.0	181.0

PFM

	A	C	G	T
01	0.337	0.1	0.484	0.08
02	0.63	0.128	0.153	0.09
03	0.698	0.094	0.121	0.087
04	0.848	0.005	0.126	0.021
05	0.072	0.052	0.834	0.042
06	0.221	0.072	0.155	0.551
07	0.037	0.001	0.962	0.0
08	0.978	0.012	0.005	0.005
09	0.908	0.006	0.084	0.002
10	0.978	0.002	0.016	0.004
11	0.048	0.01	0.937	0.005
12	0.006	0.082	0.073	0.839
13	0.134	0.131	0.553	0.183
14	0.412	0.191	0.212	0.185

PWM

	A	C	G	T
01	0.296	-0.906	0.657	-1.13
02	0.919	-0.666	-0.486	-1.012
03	1.022	-0.968	-0.715	-1.046
04	1.216	-3.603	-0.682	-2.385
05	-1.222	-1.543	1.199	-1.754
06	-0.12	-1.222	-0.473	0.786
07	-1.878	-4.507	1.343	-4.965
08	1.358	-2.889	-3.603	-3.603
09	1.285	-3.464	-1.081	-4.194
10	1.358	-4.194	-2.633	-3.764
11	-1.622	-3.047	1.316	-3.603
12	-3.464	-1.105	-1.208	1.206
13	-0.62	-0.643	0.79	-0.311
14	0.497	-0.268	-0.162	-0.3

Standard thresholds

P-value	Threshold
0.001	3.30476
0.0005	4.43921
0.0001	6.78991