FOXJ2.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXJ2.H12RSNP.0.PSM.A
Gene (human)	FOXJ2 (GeneCards)
Gene synonyms (human)	FHX
Gene (mouse)	Foxj2
Gene synonyms (mouse)	Fhx
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	nhTGTTTACdn
GC content	31.65%
Information content (bits; total / per base)	14.376 / 1.307
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	4776

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)	0.665	0.687	0.554	0.58	0.729	0.752	2.176	2.265	76.866	96.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.982	0.972	0.951	0.932	0.855	0.844
Overall, 6 experiments	best	0.998	0.997	0.992	0.989	0.97	0.961
Methyl HT-SELEX, 2 experiments	median	0.989	0.983	0.975	0.965	0.925	0.912
Methyl HT-SELEX, 2 experiments	best	0.998	0.997	0.992	0.989	0.97	0.961
Non-Methyl HT-SELEX, 4 experiments	median	0.981	0.969	0.924	0.91	0.771	0.785
Non-Methyl HT-SELEX, 4 experiments	best	0.997	0.995	0.978	0.972	0.926	0.916

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.67	0.417	0.618	0.471

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.0.PSM.A.pcm
PWM	FOXJ2.H12RSNP.0.PSM.A.pwm
PFM	FOXJ2.H12RSNP.0.PSM.A.pfm
Alignment	FOXJ2.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	FOXJ2.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	FOXJ2.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	FOXJ2.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	FOXJ2.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	FOXJ2.H12RSNP.0.PSM.A_homer_format_0.001.txt FOXJ2.H12RSNP.0.PSM.A_homer_format_0.0005.txt FOXJ2.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1186.0	809.0	1310.0	1471.0
02	1161.0	889.0	330.0	2396.0
03	0.0	0.0	0.0	4776.0
04	0.0	0.0	4776.0	0.0
05	0.0	0.0	0.0	4776.0
06	0.0	0.0	0.0	4776.0
07	0.0	0.0	106.0	4670.0
08	4776.0	0.0	0.0	0.0
09	0.0	4730.0	0.0	46.0
10	2219.25	565.25	1354.25	637.25
11	1703.0	1066.0	691.0	1316.0

PFM

	A	C	G	T
01	0.248	0.169	0.274	0.308
02	0.243	0.186	0.069	0.502
03	0.0	0.0	0.0	1.0
04	0.0	0.0	1.0	0.0
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.022	0.978
08	1.0	0.0	0.0	0.0
09	0.0	0.99	0.0	0.01
10	0.465	0.118	0.284	0.133
11	0.357	0.223	0.145	0.276

PWM

	A	C	G	T
01	-0.007	-0.388	0.093	0.208
02	-0.028	-0.294	-1.281	0.696
03	-6.336	-6.336	-6.336	1.385
04	-6.336	-6.336	1.385	-6.336
05	-6.336	-6.336	-6.336	1.385
06	-6.336	-6.336	-6.336	1.385
07	-6.336	-6.336	-2.404	1.363
08	1.385	-6.336	-6.336	-6.336
09	-6.336	1.375	-6.336	-3.213
10	0.619	-0.746	0.126	-0.626
11	0.355	-0.113	-0.546	0.097

Standard thresholds

P-value	Threshold
0.001	0.99255
0.0005	2.14109
0.0001	5.547105