PITX1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PITX1.H12INVITRO.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	10
Consensus	nGGATTAvbn
GC content	41.97%
Information content (bits; total / per base)	11.047 / 1.105
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8336

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)	0.773	0.774	0.685	0.686	0.756	0.758	2.375	2.382	0.0	0
Mouse	4 (24)	0.796	0.873	0.669	0.78	0.773	0.829	2.277	2.585	120.688	229.174

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.969	0.95	0.907	0.896	0.737	0.76
Overall, 10 experiments	best	0.986	0.976	0.983	0.969	0.973	0.957
Methyl HT-SELEX, 2 experiments	median	0.972	0.95	0.965	0.941	0.946	0.92
Methyl HT-SELEX, 2 experiments	best	0.986	0.974	0.983	0.969	0.973	0.957
Non-Methyl HT-SELEX, 8 experiments	median	0.969	0.95	0.865	0.858	0.701	0.726
Non-Methyl HT-SELEX, 8 experiments	best	0.984	0.976	0.97	0.947	0.943	0.918

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.839	0.73	0.845	0.678

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.H12INVITRO.0.PSM.A.pcm
PWM	PITX1.H12INVITRO.0.PSM.A.pwm
PFM	PITX1.H12INVITRO.0.PSM.A.pfm
Alignment	PITX1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	PITX1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	PITX1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	PITX1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	PITX1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	PITX1.H12INVITRO.0.PSM.A_homer_format_0.001.txt PITX1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt PITX1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2081.0	1780.0	2509.0	1966.0
02	756.25	197.25	6889.25	493.25
03	0.0	0.0	8336.0	0.0
04	7595.0	741.0	0.0	0.0
05	0.0	0.0	0.0	8336.0
06	0.0	0.0	0.0	8336.0
07	8274.0	0.0	5.0	57.0
08	3976.0	1286.0	2202.0	872.0
09	691.5	2936.5	3063.5	1644.5
10	1479.75	2266.75	2776.75	1812.75

PFM

	A	C	G	T
01	0.25	0.214	0.301	0.236
02	0.091	0.024	0.826	0.059
03	0.0	0.0	1.0	0.0
04	0.911	0.089	0.0	0.0
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	0.993	0.0	0.001	0.007
08	0.477	0.154	0.264	0.105
09	0.083	0.352	0.368	0.197
10	0.178	0.272	0.333	0.217

PWM

	A	C	G	T
01	-0.001	-0.157	0.185	-0.058
02	-1.012	-2.347	1.195	-1.438
03	-6.829	-6.829	1.385	-6.829
04	1.292	-1.032	-6.829	-6.829
05	-6.829	-6.829	-6.829	1.385
06	-6.829	-6.829	-6.829	1.385
07	1.378	-6.829	-5.661	-3.561
08	0.645	-0.482	0.055	-0.87
09	-1.101	0.343	0.385	-0.237
10	-0.342	0.084	0.287	-0.139

Standard thresholds

P-value	Threshold
0.001	4.344535
0.0005	5.66637
0.0001	7.89948