NFKB1.H12RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFKB1.H12RSNP.0.PS.A
Gene (human)	NFKB1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Nfkb1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	dGGGAAAKhCCC
GC content	55.5%
Information content (bits; total / per base)	15.392 / 1.283
Data sources	ChIP-Seq + HT-SELEX
Aligned words	159

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	7 (37)	0.911	0.967	0.875	0.947	0.904	0.958	3.965	4.752	508.409	796.081
Mouse	7 (35)	0.811	0.879	0.753	0.833	0.79	0.886	3.488	4.062	107.77	399.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.638	0.642	0.554	0.571	0.522	0.538
Non-Methyl HT-SELEX, 2 experiments	best	0.735	0.736	0.599	0.621	0.544	0.567

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	32.154	4.762	0.499	0.329

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: 6.1.1.1.1
HGNC	HGNC:7794
MGI	MGI:97312
EntrezGene (human)	GeneID:4790 (SSTAR profile)
EntrezGene (mouse)	GeneID:18033 (SSTAR profile)
UniProt ID (human)	NFKB1_HUMAN
UniProt ID (mouse)	NFKB1_MOUSE
UniProt AC (human)	P19838 (TFClass)
UniProt AC (mouse)	P25799 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	7 human, 7 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	NFKB1.H12RSNP.0.PS.A.pcm
PWM	NFKB1.H12RSNP.0.PS.A.pwm
PFM	NFKB1.H12RSNP.0.PS.A.pfm
Alignment	NFKB1.H12RSNP.0.PS.A.words.tsv
Threshold to P-value map	NFKB1.H12RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	NFKB1.H12RSNP.0.PS.A_jaspar_format.txt
MEME format	NFKB1.H12RSNP.0.PS.A_meme_format.meme
Transfac format	NFKB1.H12RSNP.0.PS.A_transfac_format.txt
Homer format	NFKB1.H12RSNP.0.PS.A_homer_format_0.001.txt NFKB1.H12RSNP.0.PS.A_homer_format_0.0005.txt NFKB1.H12RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	54.0	5.0	35.0	65.0
02	0.0	0.0	159.0	0.0
03	42.0	0.0	115.0	2.0
04	0.0	0.0	159.0	0.0
05	158.0	0.0	1.0	0.0
06	135.0	1.0	23.0	0.0
07	120.0	0.0	7.0	32.0
08	3.0	7.0	30.0	119.0
09	35.0	78.0	15.0	31.0
10	3.0	155.0	0.0	1.0
11	47.0	111.0	1.0	0.0
12	2.0	150.0	7.0	0.0

PFM

	A	C	G	T
01	0.34	0.031	0.22	0.409
02	0.0	0.0	1.0	0.0
03	0.264	0.0	0.723	0.013
04	0.0	0.0	1.0	0.0
05	0.994	0.0	0.006	0.0
06	0.849	0.006	0.145	0.0
07	0.755	0.0	0.044	0.201
08	0.019	0.044	0.189	0.748
09	0.22	0.491	0.094	0.195
10	0.019	0.975	0.0	0.006
11	0.296	0.698	0.006	0.0
12	0.013	0.943	0.044	0.0

PWM

	A	C	G	T
01	0.298	-1.879	-0.123	0.48
02	-3.477	-3.477	1.363	-3.477
03	0.053	-3.477	1.042	-2.53
04	-3.477	-3.477	1.363	-3.477
05	1.357	-3.477	-2.895	-3.477
06	1.201	-2.895	-0.525	-3.477
07	1.084	-3.477	-1.602	-0.209
08	-2.263	-1.602	-0.271	1.076
09	-0.123	0.659	-0.925	-0.24
10	-2.263	1.338	-3.477	-2.895
11	0.163	1.007	-2.895	-3.477
12	-2.53	1.305	-1.602	-3.477

Standard thresholds

P-value	Threshold
0.001	3.05071
0.0005	4.245215
0.0001	6.72103