PITX2.H14INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PITX2.H14INVIVO.0.SM.D
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	D

Motif length	10
Consensus	nRGATTAvbn
GC content	41.96%
Information content (bits; total / per base)	9.981 / 0.998
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8721
Previous names	PITX2.H12INVIVO.0.SM.D

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.963	0.941	0.949	0.92	0.921	0.892
Overall, 6 experiments	best	0.995	0.992	0.993	0.988	0.988	0.982
Methyl HT-SELEX, 3 experiments	median	0.987	0.978	0.982	0.97	0.975	0.959
Methyl HT-SELEX, 3 experiments	best	0.995	0.992	0.993	0.988	0.988	0.982
Non-Methyl HT-SELEX, 3 experiments	median	0.937	0.894	0.916	0.87	0.875	0.829
Non-Methyl HT-SELEX, 3 experiments	best	0.99	0.984	0.986	0.976	0.967	0.956

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.891	0.659	0.874	0.658

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	PITX2.H14INVIVO.0.SM.D.pcm
PWM	PITX2.H14INVIVO.0.SM.D.pwm
PFM	PITX2.H14INVIVO.0.SM.D.pfm
Threshold to P-value map	PITX2.H14INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	PITX2.H14INVIVO.0.SM.D_jaspar_format.txt
MEME format	PITX2.H14INVIVO.0.SM.D_meme_format.meme
Transfac format	PITX2.H14INVIVO.0.SM.D_transfac_format.txt
Homer format	PITX2.H14INVIVO.0.SM.D_homer_format_0.001.txt PITX2.H14INVIVO.0.SM.D_homer_format_0.0005.txt PITX2.H14INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2003.5	1865.5	2981.5	1870.5
02	838.25	471.25	6794.25	617.25
03	33.0	178.0	8487.0	23.0
04	7751.0	960.0	10.0	0.0
05	0.0	0.0	0.0	8721.0
06	0.0	312.0	5.0	8404.0
07	8395.0	77.0	77.0	172.0
08	3773.0	1354.0	2479.0	1115.0
09	1122.25	2721.25	3046.25	1831.25
10	1812.25	1834.25	2944.25	2130.25

PFM

	A	C	G	T
01	0.23	0.214	0.342	0.214
02	0.096	0.054	0.779	0.071
03	0.004	0.02	0.973	0.003
04	0.889	0.11	0.001	0.0
05	0.0	0.0	0.0	1.0
06	0.0	0.036	0.001	0.964
07	0.963	0.009	0.009	0.02
08	0.433	0.155	0.284	0.128
09	0.129	0.312	0.349	0.21
10	0.208	0.21	0.338	0.244

PWM

	A	C	G	T
01	-0.084	-0.156	0.313	-0.153
02	-0.954	-1.528	1.136	-1.259
03	-4.125	-2.494	1.358	-4.459
04	1.268	-0.819	-5.181	-6.869
05	-6.869	-6.869	-6.869	1.386
06	-6.869	-1.938	-5.705	1.348
07	1.347	-3.315	-3.315	-2.528
08	0.548	-0.476	0.128	-0.67
09	-0.663	0.221	0.334	-0.174
10	-0.185	-0.173	0.3	-0.023

Standard thresholds

P-value	Threshold
0.001	4.93548
0.0005	5.79453
0.0001	7.837215