NFIC.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFIC.H12INVIVO.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	9
Consensus	vWGCCARvh
GC content	57.51%
Information content (bits; total / per base)	9.456 / 1.051
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	991

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)	0.818	0.869	0.674	0.749	0.72	0.764	1.79	2.006	98.409	451.032
Mouse	2 (6)	0.762	0.791	0.614	0.643	0.641	0.664	1.579	1.617	5.921	14.387

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.98	0.964	0.971	0.952	0.96	0.937
Overall, 2 experiments	best	0.982	0.969	0.976	0.96	0.967	0.947
Methyl HT-SELEX, 1 experiments	median	0.982	0.969	0.976	0.96	0.967	0.947
Methyl HT-SELEX, 1 experiments	best	0.982	0.969	0.976	0.96	0.967	0.947
Non-Methyl HT-SELEX, 1 experiments	median	0.978	0.959	0.967	0.945	0.954	0.928
Non-Methyl HT-SELEX, 1 experiments	best	0.978	0.959	0.967	0.945	0.954	0.928

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.957	10.844	0.134	0.058

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.853	0.451	0.835	0.545
batch 2	0.824	0.556	0.862	0.669

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

PCM	NFIC.H12INVIVO.1.PSM.A.pcm
PWM	NFIC.H12INVIVO.1.PSM.A.pwm
PFM	NFIC.H12INVIVO.1.PSM.A.pfm
Alignment	NFIC.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	NFIC.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	NFIC.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	NFIC.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	NFIC.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	NFIC.H12INVIVO.1.PSM.A_homer_format_0.001.txt NFIC.H12INVIVO.1.PSM.A_homer_format_0.0005.txt NFIC.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	148.0	257.0	445.0	141.0
02	222.0	9.0	104.0	656.0
03	2.0	13.0	958.0	18.0
04	8.0	973.0	6.0	4.0
05	4.0	978.0	1.0	8.0
06	965.0	12.0	2.0	12.0
07	572.0	8.0	405.0	6.0
08	250.0	210.0	465.0	66.0
09	386.0	147.0	136.0	322.0

PFM

	A	C	G	T
01	0.149	0.259	0.449	0.142
02	0.224	0.009	0.105	0.662
03	0.002	0.013	0.967	0.018
04	0.008	0.982	0.006	0.004
05	0.004	0.987	0.001	0.008
06	0.974	0.012	0.002	0.012
07	0.577	0.008	0.409	0.006
08	0.252	0.212	0.469	0.067
09	0.39	0.148	0.137	0.325

PWM

	A	C	G	T
01	-0.511	0.036	0.583	-0.558
02	-0.109	-3.147	-0.859	0.969
03	-4.204	-2.83	1.347	-2.537
04	-3.245	1.363	-3.475	-3.775
05	-3.775	1.368	-4.517	-3.245
06	1.355	-2.9	-4.204	-2.9
07	0.833	-3.245	0.489	-3.475
08	0.009	-0.164	0.626	-1.304
09	0.441	-0.517	-0.594	0.261

Standard thresholds

P-value	Threshold
0.001	5.00763
0.0005	6.16921
0.0001	7.545925