PITX2.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PITX2.H12RSNP.0.SM.B
Gene (human)	PITX2 (GeneCards)
Gene synonyms (human)	ARP1, RGS, RIEG, RIEG1
Gene (mouse)	Pitx2
Gene synonyms (mouse)	Arp1, Brx1, Otlx2, Ptx2, Rgs
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	14
Consensus	nnddGGATTARbdn
GC content	47.19%
Information content (bits; total / per base)	13.4 / 0.957
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9990

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.96	0.932	0.942	0.911	0.902	0.871
Overall, 6 experiments	best	0.995	0.989	0.993	0.988	0.988	0.981
Methyl HT-SELEX, 3 experiments	median	0.983	0.969	0.977	0.961	0.95	0.931
Methyl HT-SELEX, 3 experiments	best	0.995	0.989	0.993	0.988	0.988	0.981
Non-Methyl HT-SELEX, 3 experiments	median	0.936	0.895	0.906	0.862	0.853	0.81
Non-Methyl HT-SELEX, 3 experiments	best	0.989	0.981	0.986	0.975	0.959	0.947

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.899	0.74	0.882	0.67

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	Paired-related HD {3.1.3} (TFClass)
TF subfamily	PITX {3.1.3.19} (TFClass)
TFClass ID	TFClass: 3.1.3.19.2
HGNC	HGNC:9005
MGI	MGI:109340
EntrezGene (human)	GeneID:5308 (SSTAR profile)
EntrezGene (mouse)	GeneID:18741 (SSTAR profile)
UniProt ID (human)	PITX2_HUMAN
UniProt ID (mouse)	PITX2_MOUSE
UniProt AC (human)	Q99697 (TFClass)
UniProt AC (mouse)	P97474 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	3

PCM	PITX2.H12RSNP.0.SM.B.pcm
PWM	PITX2.H12RSNP.0.SM.B.pwm
PFM	PITX2.H12RSNP.0.SM.B.pfm
Alignment	PITX2.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	PITX2.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	PITX2.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	PITX2.H12RSNP.0.SM.B_meme_format.meme
Transfac format	PITX2.H12RSNP.0.SM.B_transfac_format.txt
Homer format	PITX2.H12RSNP.0.SM.B_homer_format_0.001.txt PITX2.H12RSNP.0.SM.B_homer_format_0.0005.txt PITX2.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2380.25	1968.25	3331.25	2310.25
02	2734.5	2079.5	3421.5	1754.5
03	3361.0	1294.0	3835.0	1500.0
04	1704.0	1378.0	5456.0	1452.0
05	81.0	15.0	9840.0	54.0
06	21.0	7.0	9958.0	4.0
07	9971.0	16.0	2.0	1.0
08	0.0	2.0	1.0	9987.0
09	1.0	4.0	0.0	9985.0
10	9986.0	1.0	2.0	1.0
11	4652.0	230.0	4697.0	411.0
12	636.0	2977.0	3543.0	2834.0
13	1515.75	1480.75	4792.75	2200.75
14	1991.0	1878.0	3791.0	2330.0

PFM

	A	C	G	T
01	0.238	0.197	0.333	0.231
02	0.274	0.208	0.342	0.176
03	0.336	0.13	0.384	0.15
04	0.171	0.138	0.546	0.145
05	0.008	0.002	0.985	0.005
06	0.002	0.001	0.997	0.0
07	0.998	0.002	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	0.0	0.999
10	1.0	0.0	0.0	0.0
11	0.466	0.023	0.47	0.041
12	0.064	0.298	0.355	0.284
13	0.152	0.148	0.48	0.22
14	0.199	0.188	0.379	0.233

PWM

	A	C	G	T
01	-0.048	-0.238	0.288	-0.078
02	0.091	-0.183	0.315	-0.353
03	0.297	-0.657	0.429	-0.509
04	-0.382	-0.594	0.781	-0.542
05	-3.401	-4.973	1.37	-3.793
06	-4.675	-5.594	1.382	-5.983
07	1.384	-4.917	-6.365	-6.629
08	-6.99	-6.365	-6.629	1.385
09	-6.629	-5.983	-6.99	1.385
10	1.385	-6.629	-6.365	-6.629
11	0.622	-2.376	0.631	-1.8
12	-1.365	0.175	0.349	0.126
13	-0.499	-0.522	0.651	-0.126
14	-0.226	-0.285	0.417	-0.069

Standard thresholds

P-value	Threshold
0.001	1.66691
0.0005	2.97686
0.0001	7.392415