NFIC.H13RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFIC.H13RSNP.1.PSM.A
Gene (human)	NFIC (GeneCards)
Gene synonyms (human)	NFI
Gene (mouse)	Nfic
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	8
Consensus	vWGCCAAR
GC content	60.71%
Information content (bits; total / per base)	10.265 / 1.283
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000
Previous names	NFIC.H12RSNP.1.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)	0.808	0.836	0.666	0.699	0.704	0.74	1.623	1.8	92.284	413.009
Mouse	2 (6)	0.749	0.781	0.609	0.63	0.627	0.659	1.382	1.497	4.0	17.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.967	0.943	0.961	0.932	0.952	0.921
Overall, 2 experiments	best	0.972	0.952	0.968	0.944	0.96	0.933
Methyl HT-SELEX, 1 experiments	median	0.972	0.952	0.968	0.944	0.96	0.933
Methyl HT-SELEX, 1 experiments	best	0.972	0.952	0.968	0.944	0.96	0.933
Non-Methyl HT-SELEX, 1 experiments	median	0.961	0.933	0.954	0.921	0.944	0.908
Non-Methyl HT-SELEX, 1 experiments	best	0.961	0.933	0.954	0.921	0.944	0.908

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.933	15.262	0.139	0.054

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.869	0.479	0.87	0.577
batch 2	0.849	0.568	0.891	0.686

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.1.PSM.A.pcm
PWM	NFIC.H13RSNP.1.PSM.A.pwm
PFM	NFIC.H13RSNP.1.PSM.A.pfm
Threshold to P-value map	NFIC.H13RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	NFIC.H13RSNP.1.PSM.A_jaspar_format.txt
MEME format	NFIC.H13RSNP.1.PSM.A_meme_format.meme
Transfac format	NFIC.H13RSNP.1.PSM.A_transfac_format.txt
Homer format	NFIC.H13RSNP.1.PSM.A_homer_format_0.001.txt NFIC.H13RSNP.1.PSM.A_homer_format_0.0005.txt NFIC.H13RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	149.0	420.0	292.0	139.0
02	292.0	6.0	61.0	641.0
03	1.0	1.0	986.0	12.0
04	2.0	997.0	0.0	1.0
05	0.0	1000.0	0.0	0.0
06	994.0	6.0	0.0	0.0
07	632.0	4.0	364.0	0.0
08	255.0	137.0	583.0	25.0

PFM

	A	C	G	T
01	0.149	0.42	0.292	0.139
02	0.292	0.006	0.061	0.641
03	0.001	0.001	0.986	0.012
04	0.002	0.997	0.0	0.001
05	0.0	1.0	0.0	0.0
06	0.994	0.006	0.0	0.0
07	0.632	0.004	0.364	0.0
08	0.255	0.137	0.583	0.025

PWM

	A	C	G	T
01	-0.513	0.516	0.154	-0.582
02	0.154	-3.484	-1.39	0.937
03	-4.525	-4.525	1.367	-2.909
04	-4.213	1.378	-4.982	-4.525
05	-4.982	1.381	-4.982	-4.982
06	1.375	-3.484	-4.982	-4.982
07	0.923	-3.783	0.374	-4.982
08	0.02	-0.596	0.843	-2.243

Standard thresholds

P-value	Threshold
0.001	4.639325
0.0005	6.25436
0.0001	7.66746