FOXJ2.H12RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXJ2.H12RSNP.1.SM.B
Gene (human)	FOXJ2 (GeneCards)
Gene synonyms (human)	FHX
Gene (mouse)	Foxj2
Gene synonyms (mouse)	Fhx
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	17
Consensus	nhTGTTTACAACAWhvn
GC content	27.01%
Information content (bits; total / per base)	22.316 / 1.313
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	357

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	1 (6)	0.501	0.503	0.337	0.339	0.599	0.638	1.469	1.612	9.204	12.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.966	0.955	0.893	0.875	0.78	0.774
Overall, 6 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999
Methyl HT-SELEX, 2 experiments	median	0.993	0.99	0.966	0.959	0.908	0.906
Methyl HT-SELEX, 2 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999
Non-Methyl HT-SELEX, 4 experiments	median	0.893	0.863	0.797	0.771	0.691	0.686
Non-Methyl HT-SELEX, 4 experiments	best	1.0	1.0	1.0	1.0	0.959	0.962

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.746	0.535	0.785	0.57

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Fork head/winged helix factors {3.3} (TFClass)
TF family	FOX {3.3.1} (TFClass)
TF subfamily	FOXJ {3.3.1.10} (TFClass)
TFClass ID	TFClass: 3.3.1.10.2
HGNC	HGNC:24818
MGI	MGI:1926805
EntrezGene (human)	GeneID:55810 (SSTAR profile)
EntrezGene (mouse)	GeneID:60611 (SSTAR profile)
UniProt ID (human)	FOXJ2_HUMAN
UniProt ID (mouse)	FOXJ2_MOUSE
UniProt AC (human)	Q9P0K8 (TFClass)
UniProt AC (mouse)	Q9ES18 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	FOXJ2.H12RSNP.1.SM.B.pcm
PWM	FOXJ2.H12RSNP.1.SM.B.pwm
PFM	FOXJ2.H12RSNP.1.SM.B.pfm
Alignment	FOXJ2.H12RSNP.1.SM.B.words.tsv
Threshold to P-value map	FOXJ2.H12RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	FOXJ2.H12RSNP.1.SM.B_jaspar_format.txt
MEME format	FOXJ2.H12RSNP.1.SM.B_meme_format.meme
Transfac format	FOXJ2.H12RSNP.1.SM.B_transfac_format.txt
Homer format	FOXJ2.H12RSNP.1.SM.B_homer_format_0.001.txt FOXJ2.H12RSNP.1.SM.B_homer_format_0.0005.txt FOXJ2.H12RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	116.25	47.25	89.25	104.25
02	75.25	59.25	26.25	196.25
03	2.0	2.0	0.0	353.0
04	127.0	0.0	230.0	0.0
05	0.0	0.0	0.0	357.0
06	0.0	0.0	1.0	356.0
07	0.0	0.0	2.0	355.0
08	357.0	0.0	0.0	0.0
09	0.0	357.0	0.0	0.0
10	357.0	0.0	0.0	0.0
11	356.0	0.0	0.0	1.0
12	0.0	342.0	0.0	15.0
13	357.0	0.0	0.0	0.0
14	272.0	20.0	15.0	50.0
15	98.0	128.0	27.0	104.0
16	169.0	77.0	70.0	41.0
17	139.75	70.75	75.75	70.75

PFM

	A	C	G	T
01	0.326	0.132	0.25	0.292
02	0.211	0.166	0.074	0.55
03	0.006	0.006	0.0	0.989
04	0.356	0.0	0.644	0.0
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.003	0.997
07	0.0	0.0	0.006	0.994
08	1.0	0.0	0.0	0.0
09	0.0	1.0	0.0	0.0
10	1.0	0.0	0.0	0.0
11	0.997	0.0	0.0	0.003
12	0.0	0.958	0.0	0.042
13	1.0	0.0	0.0	0.0
14	0.762	0.056	0.042	0.14
15	0.275	0.359	0.076	0.291
16	0.473	0.216	0.196	0.115
17	0.391	0.198	0.212	0.198

PWM

	A	C	G	T
01	0.261	-0.622	0.0	0.153
02	-0.168	-0.402	-1.186	0.779
03	-3.264	-3.264	-4.123	1.363
04	0.348	-4.123	0.937	-4.123
05	-4.123	-4.123	-4.123	1.374
06	-4.123	-4.123	-3.604	1.371
07	-4.123	-4.123	-3.264	1.368
08	1.374	-4.123	-4.123	-4.123
09	-4.123	1.374	-4.123	-4.123
10	1.374	-4.123	-4.123	-4.123
11	1.371	-4.123	-4.123	-3.604
12	-4.123	1.331	-4.123	-1.706
13	1.374	-4.123	-4.123	-4.123
14	1.103	-1.441	-1.706	-0.567
15	0.092	0.356	-1.159	0.151
16	0.631	-0.145	-0.239	-0.759
17	0.443	-0.228	-0.161	-0.228

Standard thresholds

P-value	Threshold
0.001	-2.52679
0.0005	-0.91499
0.0001	2.90451