NFKB2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFKB2.H12INVIVO.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	dGGGRAAdYCCCn
GC content	59.42%
Information content (bits; total / per base)	13.347 / 1.027
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000

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)	0.907	0.95	0.856	0.904	0.865	0.913	3.705	4.069	439.417	492.444

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.907	0.915	0.801	0.819	0.689	0.717
Overall, 2 experiments	best	0.996	0.993	0.975	0.97	0.83	0.844
Methyl HT-SELEX, 1 experiments	median	0.996	0.993	0.975	0.97	0.83	0.844
Methyl HT-SELEX, 1 experiments	best	0.996	0.993	0.975	0.97	0.83	0.844
Non-Methyl HT-SELEX, 1 experiments	median	0.819	0.837	0.626	0.668	0.548	0.59
Non-Methyl HT-SELEX, 1 experiments	best	0.819	0.837	0.626	0.668	0.548	0.59

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.949	0.502	0.935	0.649
batch 2	0.776	0.445	0.821	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.H12INVIVO.0.PSM.A.pcm
PWM	NFKB2.H12INVIVO.0.PSM.A.pwm
PFM	NFKB2.H12INVIVO.0.PSM.A.pfm
Alignment	NFKB2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	NFKB2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	NFKB2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	NFKB2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	NFKB2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	NFKB2.H12INVIVO.0.PSM.A_homer_format_0.001.txt NFKB2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt NFKB2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	420.0	141.0	237.0	202.0
02	81.0	21.0	804.0	94.0
03	27.0	5.0	955.0	13.0
04	33.0	15.0	938.0	14.0
05	616.0	9.0	363.0	12.0
06	850.0	83.0	60.0	7.0
07	960.0	33.0	7.0	0.0
08	150.0	122.0	314.0	414.0
09	91.0	453.0	11.0	445.0
10	73.0	875.0	25.0	27.0
11	29.0	945.0	16.0	10.0
12	64.0	902.0	8.0	26.0
13	257.0	231.0	152.0	360.0

PFM

	A	C	G	T
01	0.42	0.141	0.237	0.202
02	0.081	0.021	0.804	0.094
03	0.027	0.005	0.955	0.013
04	0.033	0.015	0.938	0.014
05	0.616	0.009	0.363	0.012
06	0.85	0.083	0.06	0.007
07	0.96	0.033	0.007	0.0
08	0.15	0.122	0.314	0.414
09	0.091	0.453	0.011	0.445
10	0.073	0.875	0.025	0.027
11	0.029	0.945	0.016	0.01
12	0.064	0.902	0.008	0.026
13	0.257	0.231	0.152	0.36

PWM

	A	C	G	T
01	0.516	-0.567	-0.053	-0.212
02	-1.113	-2.405	1.163	-0.967
03	-2.171	-3.622	1.335	-2.839
04	-1.981	-2.711	1.317	-2.773
05	0.898	-3.156	0.371	-2.909
06	1.219	-1.089	-1.406	-3.362
07	1.34	-1.981	-3.362	-4.982
08	-0.506	-0.71	0.227	0.502
09	-0.999	0.591	-2.985	0.574
10	-1.215	1.248	-2.243	-2.171
11	-2.103	1.325	-2.653	-3.066
12	-1.343	1.278	-3.253	-2.206
13	0.027	-0.078	-0.493	0.363

Standard thresholds

P-value	Threshold
0.001	3.65921
0.0005	4.73391
0.0001	6.94371