PITX1.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PITX1.H12RSNP.0.PSM.A
Gene (human)	PITX1 (GeneCards)
Gene synonyms (human)	BFT, PTX1
Gene (mouse)	Pitx1
Gene synonyms (mouse)	Bft, Potx, Ptx1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	nnbGGATTARbbb
GC content	44.93%
Information content (bits; total / per base)	12.503 / 0.962
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	2437

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 (2)	0.763	0.764	0.671	0.672	0.77	0.772	2.553	2.564	0.0	0
Mouse	4 (24)	0.785	0.863	0.64	0.762	0.77	0.829	2.372	2.695	114.092	197.119

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.968	0.948	0.901	0.89	0.732	0.756
Overall, 10 experiments	best	0.985	0.971	0.983	0.968	0.971	0.955
Methyl HT-SELEX, 2 experiments	median	0.97	0.946	0.964	0.938	0.939	0.912
Methyl HT-SELEX, 2 experiments	best	0.985	0.971	0.983	0.968	0.971	0.955
Non-Methyl HT-SELEX, 8 experiments	median	0.968	0.948	0.861	0.852	0.696	0.722
Non-Methyl HT-SELEX, 8 experiments	best	0.983	0.971	0.969	0.947	0.938	0.913

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.854	0.755	0.85	0.686

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: 3.1.3.19.1
HGNC	HGNC:9004
MGI	MGI:107374
EntrezGene (human)	GeneID:5307 (SSTAR profile)
EntrezGene (mouse)	GeneID:18740 (SSTAR profile)
UniProt ID (human)	PITX1_HUMAN
UniProt ID (mouse)	PITX1_MOUSE
UniProt AC (human)	P78337 (TFClass)
UniProt AC (mouse)	P70314 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 4 mouse
HT-SELEX	8
Methyl-HT-SELEX	2

PCM	PITX1.H12RSNP.0.PSM.A.pcm
PWM	PITX1.H12RSNP.0.PSM.A.pwm
PFM	PITX1.H12RSNP.0.PSM.A.pfm
Alignment	PITX1.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	PITX1.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	PITX1.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	PITX1.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	PITX1.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	PITX1.H12RSNP.0.PSM.A_homer_format_0.001.txt PITX1.H12RSNP.0.PSM.A_homer_format_0.0005.txt PITX1.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	570.75	548.75	792.75	524.75
02	550.75	453.75	929.75	502.75
03	390.0	417.0	1207.0	423.0
04	116.0	26.0	2257.0	38.0
05	3.0	0.0	2433.0	1.0
06	2424.0	12.0	1.0	0.0
07	0.0	0.0	0.0	2437.0
08	0.0	0.0	0.0	2437.0
09	2427.0	3.0	1.0	6.0
10	1452.0	141.0	635.0	209.0
11	293.0	465.0	965.0	714.0
12	440.5	503.5	987.5	505.5
13	451.5	469.5	986.5	529.5

PFM

	A	C	G	T
01	0.234	0.225	0.325	0.215
02	0.226	0.186	0.382	0.206
03	0.16	0.171	0.495	0.174
04	0.048	0.011	0.926	0.016
05	0.001	0.0	0.998	0.0
06	0.995	0.005	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.996	0.001	0.0	0.002
10	0.596	0.058	0.261	0.086
11	0.12	0.191	0.396	0.293
12	0.181	0.207	0.405	0.207
13	0.185	0.193	0.405	0.217

PWM

	A	C	G	T
01	-0.065	-0.104	0.263	-0.149
02	-0.101	-0.294	0.422	-0.191
03	-0.444	-0.378	0.682	-0.363
04	-1.645	-3.085	1.307	-2.728
05	-4.816	-5.748	1.382	-5.334
06	1.379	-3.78	-5.334	-5.748
07	-5.748	-5.748	-5.748	1.384
08	-5.748	-5.748	-5.748	1.384
09	1.38	-4.816	-5.334	-4.342
10	0.867	-1.453	0.041	-1.064
11	-0.729	-0.269	0.459	0.158
12	-0.323	-0.19	0.482	-0.186
13	-0.299	-0.26	0.481	-0.14

Standard thresholds

P-value	Threshold
0.001	2.88226
0.0005	4.291415
0.0001	7.723825