PITX1.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PITX1.H12INVIVO.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	9
Consensus	RGGATTAdn
GC content	42.63%
Information content (bits; total / per base)	10.139 / 1.127
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1037

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)	0.774	0.775	0.68	0.683	0.76	0.762	2.347	2.358	0.0	0
Mouse	4 (24)	0.808	0.894	0.676	0.807	0.787	0.855	2.351	2.707	134.222	242.149

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.964	0.943	0.901	0.886	0.735	0.756
Overall, 10 experiments	best	0.984	0.97	0.979	0.963	0.963	0.945
Methyl HT-SELEX, 2 experiments	median	0.968	0.944	0.959	0.933	0.938	0.909
Methyl HT-SELEX, 2 experiments	best	0.984	0.97	0.979	0.963	0.963	0.945
Non-Methyl HT-SELEX, 8 experiments	median	0.964	0.943	0.861	0.849	0.7	0.722
Non-Methyl HT-SELEX, 8 experiments	best	0.98	0.968	0.962	0.938	0.934	0.906

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.829	0.712	0.842	0.666

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.H12INVIVO.0.PSM.A.pcm
PWM	PITX1.H12INVIVO.0.PSM.A.pwm
PFM	PITX1.H12INVIVO.0.PSM.A.pfm
Alignment	PITX1.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	PITX1.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	PITX1.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	PITX1.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	PITX1.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	PITX1.H12INVIVO.0.PSM.A_homer_format_0.001.txt PITX1.H12INVIVO.0.PSM.A_homer_format_0.0005.txt PITX1.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	338.0	12.0	530.0	157.0
02	98.0	1.0	924.0	14.0
03	31.0	3.0	1001.0	2.0
04	706.0	316.0	7.0	8.0
05	1.0	1.0	2.0	1033.0
06	21.0	41.0	14.0	961.0
07	947.0	0.0	8.0	82.0
08	441.0	65.0	448.0	83.0
09	259.0	281.0	325.0	172.0

PFM

	A	C	G	T
01	0.326	0.012	0.511	0.151
02	0.095	0.001	0.891	0.014
03	0.03	0.003	0.965	0.002
04	0.681	0.305	0.007	0.008
05	0.001	0.001	0.002	0.996
06	0.02	0.04	0.014	0.927
07	0.913	0.0	0.008	0.079
08	0.425	0.063	0.432	0.08
09	0.25	0.271	0.313	0.166

PWM

	A	C	G	T
01	0.264	-2.944	0.712	-0.497
02	-0.962	-4.558	1.266	-2.809
03	-2.076	-4.009	1.346	-4.246
04	0.998	0.197	-3.397	-3.289
05	-4.558	-4.558	-4.246	1.377
06	-2.441	-1.809	-2.809	1.305
07	1.291	-5.013	-3.289	-1.137
08	0.529	-1.364	0.544	-1.125
09	-0.001	0.08	0.225	-0.407

Standard thresholds

P-value	Threshold
0.001	4.68443
0.0005	5.636105
0.0001	7.708135