NFIC.H12INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFIC.H12INVITRO.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	10
Consensus	ndYGCCAAnd
GC content	52.05%
Information content (bits; total / per base)	11.072 / 1.107
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8763

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)	0.781	0.827	0.604	0.678	0.646	0.691	1.536	1.715	87.143	378.208
Mouse	2 (6)	0.756	0.768	0.614	0.618	0.633	0.638	1.527	1.579	6.523	12.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.983	0.971	0.976	0.959	0.963	0.943
Overall, 2 experiments	best	0.986	0.976	0.983	0.97	0.974	0.959
Methyl HT-SELEX, 1 experiments	median	0.986	0.976	0.983	0.97	0.974	0.959
Methyl HT-SELEX, 1 experiments	best	0.986	0.976	0.983	0.97	0.974	0.959
Non-Methyl HT-SELEX, 1 experiments	median	0.98	0.966	0.968	0.949	0.951	0.927
Non-Methyl HT-SELEX, 1 experiments	best	0.98	0.966	0.968	0.949	0.951	0.927

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.3	11.101	0.133	0.062

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.83	0.391	0.834	0.528
batch 2	0.813	0.522	0.822	0.652

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.H12INVITRO.1.PSM.A.pcm
PWM	NFIC.H12INVITRO.1.PSM.A.pwm
PFM	NFIC.H12INVITRO.1.PSM.A.pfm
Alignment	NFIC.H12INVITRO.1.PSM.A.words.tsv
Threshold to P-value map	NFIC.H12INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	NFIC.H12INVITRO.1.PSM.A_jaspar_format.txt
MEME format	NFIC.H12INVITRO.1.PSM.A_meme_format.meme
Transfac format	NFIC.H12INVITRO.1.PSM.A_transfac_format.txt
Homer format	NFIC.H12INVITRO.1.PSM.A_homer_format_0.001.txt NFIC.H12INVITRO.1.PSM.A_homer_format_0.0005.txt NFIC.H12INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2201.25	2475.25	2253.25	1833.25
02	2671.25	755.25	3243.25	2093.25
03	643.0	2124.0	42.0	5954.0
04	0.0	0.0	8763.0	0.0
05	0.0	8763.0	0.0	0.0
06	0.0	8763.0	0.0	0.0
07	8763.0	0.0	0.0	0.0
08	8722.0	0.0	41.0	0.0
09	1758.75	2542.75	2971.75	1489.75
10	2681.75	1323.75	1549.75	3207.75

PFM

	A	C	G	T
01	0.251	0.282	0.257	0.209
02	0.305	0.086	0.37	0.239
03	0.073	0.242	0.005	0.679
04	0.0	0.0	1.0	0.0
05	0.0	1.0	0.0	0.0
06	0.0	1.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.995	0.0	0.005	0.0
09	0.201	0.29	0.339	0.17
10	0.306	0.151	0.177	0.366

PWM

	A	C	G	T
01	0.005	0.122	0.028	-0.178
02	0.198	-1.063	0.392	-0.045
03	-1.223	-0.031	-3.903	0.999
04	-6.873	-6.873	1.386	-6.873
05	-6.873	1.386	-6.873	-6.873
06	-6.873	1.386	-6.873	-6.873
07	1.386	-6.873	-6.873	-6.873
08	1.381	-6.873	-3.926	-6.873
09	-0.219	0.149	0.305	-0.385
10	0.202	-0.503	-0.346	0.381

Standard thresholds

P-value	Threshold
0.001	2.598675
0.0005	5.98829
0.0001	7.94703