NFIB.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFIB.H12RSNP.0.PSM.A
Gene (human)	NFIB (GeneCards)
Gene synonyms (human)
Gene (mouse)	Nfib
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	20
Consensus	nnTTGGCAhCdTGCCAAvnn
GC content	54.1%
Information content (bits; total / per base)	23.615 / 1.181
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	412

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	2 (14)	0.823	0.881	0.824	0.885	0.961	0.996	6.668	7.308	817.806	1257.658
Mouse	4 (28)	0.554	0.696	0.453	0.673	0.756	0.943	2.561	4.898	114.903	362.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.87	0.88	0.804	0.817	0.777	0.788
Overall, 4 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, 3 experiments	median	0.74	0.76	0.609	0.634	0.554	0.577
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.571	0.154	0.218	0.147

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: 7.1.2.0.2
HGNC	HGNC:7785
MGI	MGI:103188
EntrezGene (human)	GeneID:4781 (SSTAR profile)
EntrezGene (mouse)	GeneID:18028 (SSTAR profile)
UniProt ID (human)	NFIB_HUMAN
UniProt ID (mouse)	NFIB_MOUSE
UniProt AC (human)	O00712 (TFClass)
UniProt AC (mouse)	P97863 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 4 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

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

PCM

	A	C	G	T
01	154.25	82.25	88.25	87.25
02	55.25	130.25	124.25	102.25
03	3.0	104.0	2.0	303.0
04	0.0	0.0	0.0	412.0
05	0.0	0.0	412.0	0.0
06	0.0	1.0	411.0	0.0
07	0.0	412.0	0.0	0.0
08	393.0	0.0	6.0	13.0
09	117.0	145.0	41.0	109.0
10	190.0	222.0	0.0	0.0
11	58.0	41.0	243.0	70.0
12	2.0	0.0	0.0	410.0
13	0.0	0.0	412.0	0.0
14	0.0	412.0	0.0	0.0
15	0.0	412.0	0.0	0.0
16	412.0	0.0	0.0	0.0
17	309.0	6.0	97.0	0.0
18	81.0	159.0	107.0	65.0
19	85.25	117.25	66.25	143.25
20	101.5	132.5	71.5	106.5

PFM

	A	C	G	T
01	0.374	0.2	0.214	0.212
02	0.134	0.316	0.302	0.248
03	0.007	0.252	0.005	0.735
04	0.0	0.0	0.0	1.0
05	0.0	0.0	1.0	0.0
06	0.0	0.002	0.998	0.0
07	0.0	1.0	0.0	0.0
08	0.954	0.0	0.015	0.032
09	0.284	0.352	0.1	0.265
10	0.461	0.539	0.0	0.0
11	0.141	0.1	0.59	0.17
12	0.005	0.0	0.0	0.995
13	0.0	0.0	1.0	0.0
14	0.0	1.0	0.0	0.0
15	0.0	1.0	0.0	0.0
16	1.0	0.0	0.0	0.0
17	0.75	0.015	0.235	0.0
18	0.197	0.386	0.26	0.158
19	0.207	0.285	0.161	0.348
20	0.246	0.322	0.174	0.258

PWM

	A	C	G	T
01	0.399	-0.221	-0.152	-0.163
02	-0.61	0.232	0.185	-0.007
03	-3.144	0.01	-3.395	1.069
04	-4.24	-4.24	-4.24	1.375
05	-4.24	-4.24	1.375	-4.24
06	-4.24	-3.731	1.373	-4.24
07	-4.24	1.375	-4.24	-4.24
08	1.328	-4.24	-2.634	-1.975
09	0.126	0.338	-0.9	0.056
10	0.606	0.76	-4.24	-4.24
11	-0.563	-0.9	0.85	-0.379
12	-3.395	-4.24	-4.24	1.371
13	-4.24	-4.24	1.375	-4.24
14	-4.24	1.375	-4.24	-4.24
15	-4.24	1.375	-4.24	-4.24
16	1.375	-4.24	-4.24	-4.24
17	1.089	-2.634	-0.059	-4.24
18	-0.236	0.429	0.038	-0.452
19	-0.186	0.128	-0.433	0.326
20	-0.014	0.249	-0.359	0.033

Standard thresholds

P-value	Threshold
0.001	-4.20834
0.0005	-2.14409
0.0001	1.50931