NFKB2.H13RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFKB2.H13RSNP.0.PSM.A
Gene (human)	NFKB2 (GeneCards)
Gene synonyms (human)	LYT10
Gene (mouse)	Nfkb2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	dGGGRAAdYCCCh
GC content	59.28%
Information content (bits; total / per base)	13.697 / 1.054
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000
Previous names	NFKB2.H12RSNP.0.PSM.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	2 (10)	0.898	0.945	0.85	0.902	0.859	0.913	3.716	3.936	432.145	483.523

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.908	0.915	0.802	0.82	0.686	0.716
Overall, 2 experiments	best	0.996	0.993	0.976	0.971	0.822	0.84
Methyl HT-SELEX, 1 experiments	median	0.996	0.993	0.976	0.971	0.822	0.84
Methyl HT-SELEX, 1 experiments	best	0.996	0.993	0.976	0.971	0.822	0.84
Non-Methyl HT-SELEX, 1 experiments	median	0.82	0.837	0.628	0.669	0.551	0.591
Non-Methyl HT-SELEX, 1 experiments	best	0.82	0.837	0.628	0.669	0.551	0.591

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.941	0.546	0.937	0.632
batch 2	0.82	0.507	0.81	0.637

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	Rel homology region (RHR) factors {6.1} (TFClass)
TF family	NFkappaB-related {6.1.1} (TFClass)
TF subfamily	NFkappaB p50-like {6.1.1.1} (TFClass)
TFClass ID	TFClass: 6.1.1.1.2
HGNC	HGNC:7795
MGI	MGI:1099800
EntrezGene (human)	GeneID:4791 (SSTAR profile)
EntrezGene (mouse)	GeneID:18034 (SSTAR profile)
UniProt ID (human)	NFKB2_HUMAN
UniProt ID (mouse)	NFKB2_MOUSE
UniProt AC (human)	Q00653 (TFClass)
UniProt AC (mouse)	Q9WTK5 (TFClass)
GRECO-DB-TF	yes

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

PCM	NFKB2.H13RSNP.0.PSM.A.pcm
PWM	NFKB2.H13RSNP.0.PSM.A.pwm
PFM	NFKB2.H13RSNP.0.PSM.A.pfm
Threshold to P-value map	NFKB2.H13RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	NFKB2.H13RSNP.0.PSM.A_jaspar_format.txt
MEME format	NFKB2.H13RSNP.0.PSM.A_meme_format.meme
Transfac format	NFKB2.H13RSNP.0.PSM.A_transfac_format.txt
Homer format	NFKB2.H13RSNP.0.PSM.A_homer_format_0.001.txt NFKB2.H13RSNP.0.PSM.A_homer_format_0.0005.txt NFKB2.H13RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	391.0	121.0	208.0	280.0
02	70.0	8.0	829.0	93.0
03	25.0	2.0	967.0	6.0
04	29.0	2.0	937.0	32.0
05	578.0	13.0	401.0	8.0
06	880.0	56.0	62.0	2.0
07	927.0	5.0	68.0	0.0
08	169.0	134.0	364.0	333.0
09	101.0	455.0	33.0	411.0
10	121.0	872.0	2.0	5.0
11	3.0	991.0	0.0	6.0
12	72.0	863.0	8.0	57.0
13	272.0	177.0	129.0	422.0

PFM

	A	C	G	T
01	0.391	0.121	0.208	0.28
02	0.07	0.008	0.829	0.093
03	0.025	0.002	0.967	0.006
04	0.029	0.002	0.937	0.032
05	0.578	0.013	0.401	0.008
06	0.88	0.056	0.062	0.002
07	0.927	0.005	0.068	0.0
08	0.169	0.134	0.364	0.333
09	0.101	0.455	0.033	0.411
10	0.121	0.872	0.002	0.005
11	0.003	0.991	0.0	0.006
12	0.072	0.863	0.008	0.057
13	0.272	0.177	0.129	0.422

PWM

	A	C	G	T
01	0.445	-0.718	-0.183	0.113
02	-1.255	-3.253	1.194	-0.977
03	-2.243	-4.213	1.348	-3.484
04	-2.103	-4.213	1.316	-2.01
05	0.834	-2.839	0.47	-3.253
06	1.254	-1.473	-1.374	-4.213
07	1.305	-3.622	-1.284	-4.982
08	-0.388	-0.618	0.374	0.285
09	-0.896	0.596	-1.981	0.494
10	-0.718	1.244	-4.213	-3.622
11	-3.975	1.372	-4.982	-3.484
12	-1.228	1.234	-3.253	-1.455
13	0.084	-0.342	-0.655	0.521

Standard thresholds

P-value	Threshold
0.001	3.39476
0.0005	4.519165
0.0001	6.89309