PDX1.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PDX1.H12INVIVO.0.P.B
Gene (human)	PDX1 (GeneCards)
Gene synonyms (human)	IPF1, STF1
Gene (mouse)	Pdx1
Gene synonyms (mouse)	Ipf1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	10
Consensus	TGATTRATKR
GC content	28.24%
Information content (bits; total / per base)	13.212 / 1.321
Data sources	ChIP-Seq
Aligned words	1000

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	6 (39)	0.925	0.96	0.872	0.926	0.912	0.949	3.605	4.152	473.959	634.854
Mouse	4 (26)	0.78	0.933	0.658	0.903	0.743	0.908	2.269	3.871	51.005	409.444

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.714	0.654	0.655	0.615	0.604	0.582
Overall, 4 experiments	best	0.753	0.688	0.69	0.643	0.637	0.606
Methyl HT-SELEX, 1 experiments	median	0.753	0.688	0.69	0.643	0.637	0.606
Methyl HT-SELEX, 1 experiments	best	0.753	0.688	0.69	0.643	0.637	0.606
Non-Methyl HT-SELEX, 3 experiments	median	0.691	0.634	0.631	0.596	0.581	0.566
Non-Methyl HT-SELEX, 3 experiments	best	0.737	0.674	0.68	0.633	0.627	0.599

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.615	0.118	0.62	0.413

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HOX-related {3.1.1} (TFClass)
TF subfamily	PDX {3.1.1.15} (TFClass)
TFClass ID	TFClass: 3.1.1.15.1
HGNC	HGNC:6107
MGI	MGI:102851
EntrezGene (human)	GeneID:3651 (SSTAR profile)
EntrezGene (mouse)	GeneID:18609 (SSTAR profile)
UniProt ID (human)	PDX1_HUMAN
UniProt ID (mouse)	PDX1_MOUSE
UniProt AC (human)	P52945 (TFClass)
UniProt AC (mouse)	P52946 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	6 human, 4 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	PDX1.H12INVIVO.0.P.B.pcm
PWM	PDX1.H12INVIVO.0.P.B.pwm
PFM	PDX1.H12INVIVO.0.P.B.pfm
Alignment	PDX1.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	PDX1.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	PDX1.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	PDX1.H12INVIVO.0.P.B_meme_format.meme
Transfac format	PDX1.H12INVIVO.0.P.B_transfac_format.txt
Homer format	PDX1.H12INVIVO.0.P.B_homer_format_0.001.txt PDX1.H12INVIVO.0.P.B_homer_format_0.0005.txt PDX1.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	178.0	0.0	6.0	816.0
02	31.0	0.0	966.0	3.0
03	1000.0	0.0	0.0	0.0
04	7.0	58.0	16.0	919.0
05	176.0	3.0	44.0	777.0
06	496.0	5.0	484.0	15.0
07	1000.0	0.0	0.0	0.0
08	7.0	23.0	40.0	930.0
09	42.0	38.0	629.0	291.0
10	414.0	35.0	477.0	74.0

PFM

	A	C	G	T
01	0.178	0.0	0.006	0.816
02	0.031	0.0	0.966	0.003
03	1.0	0.0	0.0	0.0
04	0.007	0.058	0.016	0.919
05	0.176	0.003	0.044	0.777
06	0.496	0.005	0.484	0.015
07	1.0	0.0	0.0	0.0
08	0.007	0.023	0.04	0.93
09	0.042	0.038	0.629	0.291
10	0.414	0.035	0.477	0.074

PWM

	A	C	G	T
01	-0.337	-4.982	-3.484	1.178
02	-2.04	-4.982	1.347	-3.975
03	1.381	-4.982	-4.982	-4.982
04	-3.362	-1.439	-2.653	1.297
05	-0.348	-3.975	-1.706	1.129
06	0.682	-3.622	0.657	-2.711
07	1.381	-4.982	-4.982	-4.982
08	-3.362	-2.32	-1.797	1.309
09	-1.75	-1.846	0.919	0.151
10	0.502	-1.925	0.643	-1.201

Standard thresholds

P-value	Threshold
0.001	3.37512
0.0005	4.639675
0.0001	7.05634