NFKB2.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFKB2.H12INVITRO.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	16
Consensus	ndRGGGGAAdYMCSdn
GC content	55.3%
Information content (bits; total / per base)	14.937 / 0.934
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8027

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)	0.893	0.939	0.847	0.886	0.831	0.886	3.338	3.643	401.6	460.387

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.915	0.921	0.817	0.831	0.718	0.739
Overall, 2 experiments	best	0.998	0.996	0.984	0.98	0.87	0.877
Methyl HT-SELEX, 1 experiments	median	0.998	0.996	0.984	0.98	0.87	0.877
Methyl HT-SELEX, 1 experiments	best	0.998	0.996	0.984	0.98	0.87	0.877
Non-Methyl HT-SELEX, 1 experiments	median	0.833	0.846	0.65	0.682	0.565	0.601
Non-Methyl HT-SELEX, 1 experiments	best	0.833	0.846	0.65	0.682	0.565	0.601

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.957	0.625	0.923	0.603
batch 2	0.783	0.422	0.784	0.613

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

PCM	NFKB2.H12INVITRO.0.PSM.A.pcm
PWM	NFKB2.H12INVITRO.0.PSM.A.pwm
PFM	NFKB2.H12INVITRO.0.PSM.A.pfm
Alignment	NFKB2.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	NFKB2.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	NFKB2.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	NFKB2.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	NFKB2.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	NFKB2.H12INVITRO.0.PSM.A_homer_format_0.001.txt NFKB2.H12INVITRO.0.PSM.A_homer_format_0.0005.txt NFKB2.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2247.75	1641.75	2310.75	1826.75
02	3644.25	913.25	1724.25	1745.25
03	4697.0	585.0	1952.0	793.0
04	11.0	6.0	8004.0	6.0
05	1.0	1.0	8025.0	0.0
06	0.0	0.0	8002.0	25.0
07	2593.0	0.0	5410.0	24.0
08	7920.0	18.0	75.0	14.0
09	6302.0	120.0	92.0	1513.0
10	1334.0	493.0	1987.0	4213.0
11	871.0	3314.0	215.0	3627.0
12	2768.0	4937.0	110.0	212.0
13	145.0	7528.0	221.0	133.0
14	345.0	6357.0	767.0	558.0
15	1423.75	1374.75	1663.75	3564.75
16	1930.5	1730.5	1443.5	2922.5

PFM

	A	C	G	T
01	0.28	0.205	0.288	0.228
02	0.454	0.114	0.215	0.217
03	0.585	0.073	0.243	0.099
04	0.001	0.001	0.997	0.001
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.997	0.003
07	0.323	0.0	0.674	0.003
08	0.987	0.002	0.009	0.002
09	0.785	0.015	0.011	0.188
10	0.166	0.061	0.248	0.525
11	0.109	0.413	0.027	0.452
12	0.345	0.615	0.014	0.026
13	0.018	0.938	0.028	0.017
14	0.043	0.792	0.096	0.07
15	0.177	0.171	0.207	0.444
16	0.241	0.216	0.18	0.364

PWM

	A	C	G	T
01	0.113	-0.201	0.141	-0.094
02	0.596	-0.786	-0.152	-0.139
03	0.85	-1.23	-0.028	-0.927
04	-5.022	-5.495	1.383	-5.495
05	-6.427	-6.427	1.385	-6.796
06	-6.796	-6.796	1.382	-4.3
07	0.256	-6.796	0.991	-4.338
08	1.372	-4.597	-3.258	-4.817
09	1.144	-2.799	-3.059	-0.282
10	-0.408	-1.4	-0.01	0.741
11	-0.833	0.501	-2.224	0.591
12	0.321	0.9	-2.885	-2.238
13	-2.613	1.321	-2.197	-2.698
14	-1.755	1.152	-0.96	-1.277
15	-0.343	-0.378	-0.187	0.574
16	-0.039	-0.148	-0.329	0.376

Standard thresholds

P-value	Threshold
0.001	1.93931
0.0005	3.44056
0.0001	6.46651