FOXJ2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	FOXJ2.H12INVIVO.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	12
Consensus	bKGTTKYYhWRd
GC content	44.82%
Information content (bits; total / per base)	8.887 / 0.741
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	449

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)	0.803	0.821	0.686	0.699	0.807	0.838	2.66	2.862	162.299	208.284

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.802	0.713	0.793	0.711	0.732	0.673
Overall, 6 experiments	best	0.835	0.756	0.812	0.737	0.786	0.701
Methyl HT-SELEX, 2 experiments	median	0.803	0.714	0.807	0.72	0.77	0.7
Methyl HT-SELEX, 2 experiments	best	0.834	0.756	0.812	0.737	0.786	0.701
Non-Methyl HT-SELEX, 4 experiments	median	0.796	0.713	0.775	0.698	0.695	0.653
Non-Methyl HT-SELEX, 4 experiments	best	0.835	0.755	0.804	0.732	0.734	0.686

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.541	0.227	0.447	0.284

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.H12INVIVO.0.PSM.A.pcm
PWM	FOXJ2.H12INVIVO.0.PSM.A.pwm
PFM	FOXJ2.H12INVIVO.0.PSM.A.pfm
Alignment	FOXJ2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	FOXJ2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	FOXJ2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	FOXJ2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	FOXJ2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	FOXJ2.H12INVIVO.0.PSM.A_homer_format_0.001.txt FOXJ2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt FOXJ2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	56.0	169.0	64.0	160.0
02	38.0	35.0	64.0	312.0
03	10.0	0.0	431.0	8.0
04	6.0	18.0	8.0	417.0
05	4.0	15.0	26.0	404.0
06	40.0	6.0	258.0	145.0
07	85.0	273.0	5.0	86.0
08	4.0	238.0	13.0	194.0
09	240.0	73.0	46.0	90.0
10	81.0	26.0	75.0	267.0
11	75.0	20.0	288.0	66.0
12	94.0	57.0	207.0	91.0

PFM

	A	C	G	T
01	0.125	0.376	0.143	0.356
02	0.085	0.078	0.143	0.695
03	0.022	0.0	0.96	0.018
04	0.013	0.04	0.018	0.929
05	0.009	0.033	0.058	0.9
06	0.089	0.013	0.575	0.323
07	0.189	0.608	0.011	0.192
08	0.009	0.53	0.029	0.432
09	0.535	0.163	0.102	0.2
10	0.18	0.058	0.167	0.595
11	0.167	0.045	0.641	0.147
12	0.209	0.127	0.461	0.203

PWM

	A	C	G	T
01	-0.682	0.405	-0.552	0.35
02	-1.057	-1.136	-0.552	1.014
03	-2.29	-4.311	1.335	-2.48
04	-2.716	-1.762	-2.48	1.303
05	-3.025	-1.929	-1.419	1.271
06	-1.008	-2.716	0.825	0.253
07	-0.274	0.881	-2.858	-0.262
08	-3.025	0.744	-2.058	0.541
09	0.753	-0.423	-0.873	-0.218
10	-0.321	-1.419	-0.397	0.859
11	-0.397	-1.665	0.934	-0.522
12	-0.175	-0.665	0.606	-0.207

Standard thresholds

P-value	Threshold
0.001	4.963765
0.0005	5.71151
0.0001	7.19172