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

Motif	NFIC.H13RSNP.0.PSM.A
Gene (human)	NFIC (GeneCards)
Gene synonyms (human)	NFI
Gene (mouse)	Nfic
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	17
Consensus	nYTGGCdnCdhGCCARn
GC content	55.28%
Information content (bits; total / per base)	16.689 / 0.982
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	2493
Previous names	NFIC.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	6 (41)	0.865	0.98	0.807	0.976	0.819	0.975	2.902	6.267	205.959	882.886
Mouse	2 (6)	0.761	0.836	0.693	0.761	0.7	0.78	2.382	2.61	9.387	33.108

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	1.0	1.0	1.0	1.0	0.999	0.999
Overall, 2 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0
Non-Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	0.999	0.998	0.998
Non-Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	0.999	0.998	0.998

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.865	15.684	0.169	0.069

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.984	0.941	0.965	0.628
batch 2	0.882	0.699	0.882	0.738

TF superclass	beta-Hairpin exposed by an alpha/beta-scaffold {7} (TFClass)
TF class	SMAD/NF-1 DNA-binding domain factors {7.1} (TFClass)
TF family	NF-1 {7.1.2} (TFClass)
TF subfamily	{7.1.2.0} (TFClass)
TFClass ID	TFClass: 7.1.2.0.3
HGNC	HGNC:7786
MGI	MGI:109591
EntrezGene (human)	GeneID:4782 (SSTAR profile)
EntrezGene (mouse)	GeneID:18029 (SSTAR profile)
UniProt ID (human)	NFIC_HUMAN
UniProt ID (mouse)	NFIC_MOUSE
UniProt AC (human)	P08651 (TFClass)
UniProt AC (mouse)	P70255 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	6 human, 2 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	NFIC.H13RSNP.0.PSM.A.pcm
PWM	NFIC.H13RSNP.0.PSM.A.pwm
PFM	NFIC.H13RSNP.0.PSM.A.pfm
Threshold to P-value map	NFIC.H13RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	NFIC.H13RSNP.0.PSM.A_jaspar_format.txt
MEME format	NFIC.H13RSNP.0.PSM.A_meme_format.meme
Transfac format	NFIC.H13RSNP.0.PSM.A_transfac_format.txt
Homer format	NFIC.H13RSNP.0.PSM.A_homer_format_0.001.txt NFIC.H13RSNP.0.PSM.A_homer_format_0.0005.txt NFIC.H13RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	508.5	791.5	662.5	530.5
02	125.25	507.25	58.25	1802.25
03	44.0	30.0	26.0	2393.0
04	35.0	32.0	2404.0	22.0
05	38.0	34.0	2388.0	33.0
06	223.0	2207.0	21.0	42.0
07	1354.0	156.0	592.0	391.0
08	770.0	605.0	352.0	766.0
09	0.0	1379.0	0.0	1114.0
10	657.0	302.0	903.0	631.0
11	374.0	573.0	259.0	1287.0
12	27.0	26.0	2238.0	202.0
13	14.0	2418.0	34.0	27.0
14	28.0	2407.0	20.0	38.0
15	2400.0	44.0	23.0	26.0
16	1845.75	67.75	491.75	87.75
17	615.5	620.5	755.5	501.5

PFM

	A	C	G	T
01	0.204	0.317	0.266	0.213
02	0.05	0.203	0.023	0.723
03	0.018	0.012	0.01	0.96
04	0.014	0.013	0.964	0.009
05	0.015	0.014	0.958	0.013
06	0.089	0.885	0.008	0.017
07	0.543	0.063	0.237	0.157
08	0.309	0.243	0.141	0.307
09	0.0	0.553	0.0	0.447
10	0.264	0.121	0.362	0.253
11	0.15	0.23	0.104	0.516
12	0.011	0.01	0.898	0.081
13	0.006	0.97	0.014	0.011
14	0.011	0.966	0.008	0.015
15	0.963	0.018	0.009	0.01
16	0.74	0.027	0.197	0.035
17	0.247	0.249	0.303	0.201

PWM

	A	C	G	T
01	-0.203	0.238	0.061	-0.161
02	-1.592	-0.205	-2.34	1.06
03	-2.61	-2.974	-3.107	1.343
04	-2.828	-2.913	1.348	-3.262
05	-2.75	-2.856	1.341	-2.884
06	-1.022	1.262	-3.305	-2.655
07	0.774	-1.376	-0.051	-0.464
08	0.211	-0.03	-0.569	0.206
09	-5.768	0.792	-5.768	0.579
10	0.053	-0.721	0.37	0.012
11	-0.509	-0.084	-0.874	0.724
12	-3.072	-3.107	1.276	-1.12
13	-3.668	1.353	-2.856	-3.072
14	-3.038	1.349	-3.349	-2.75
15	1.346	-2.61	-3.221	-3.107
16	1.084	-2.194	-0.236	-1.942
17	-0.012	-0.004	0.192	-0.217

Standard thresholds

P-value	Threshold
0.001	1.86091
0.0005	3.16966
0.0001	5.88421