PDX1.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PDX1.H12RSNP.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	TGATTRATKd
GC content	30.5%
Information content (bits; total / per base)	10.603 / 1.06
Data sources	ChIP-Seq
Aligned words	403

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)	0.914	0.95	0.86	0.915	0.894	0.934	3.471	3.987	460.721	633.208
Mouse	4 (26)	0.809	0.935	0.691	0.902	0.736	0.901	2.189	3.869	45.959	395.161

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.733	0.663	0.689	0.633	0.641	0.604
Overall, 4 experiments	best	0.773	0.698	0.733	0.668	0.693	0.64
Methyl HT-SELEX, 1 experiments	median	0.773	0.698	0.733	0.668	0.693	0.64
Methyl HT-SELEX, 1 experiments	best	0.773	0.698	0.733	0.668	0.693	0.64
Non-Methyl HT-SELEX, 3 experiments	median	0.71	0.645	0.658	0.612	0.604	0.581
Non-Methyl HT-SELEX, 3 experiments	best	0.755	0.681	0.719	0.655	0.678	0.628

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.637	0.128	0.639	0.424

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.H12RSNP.0.P.B.pcm
PWM	PDX1.H12RSNP.0.P.B.pwm
PFM	PDX1.H12RSNP.0.P.B.pfm
Alignment	PDX1.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	PDX1.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	PDX1.H12RSNP.0.P.B_jaspar_format.txt
MEME format	PDX1.H12RSNP.0.P.B_meme_format.meme
Transfac format	PDX1.H12RSNP.0.P.B_transfac_format.txt
Homer format	PDX1.H12RSNP.0.P.B_homer_format_0.001.txt PDX1.H12RSNP.0.P.B_homer_format_0.0005.txt PDX1.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	59.0	1.0	12.0	331.0
02	32.0	2.0	359.0	10.0
03	378.0	2.0	5.0	18.0
04	11.0	28.0	23.0	341.0
05	74.0	3.0	12.0	314.0
06	147.0	10.0	234.0	12.0
07	374.0	17.0	10.0	2.0
08	17.0	8.0	36.0	342.0
09	33.0	24.0	210.0	136.0
10	124.0	34.0	199.0	46.0

PFM

	A	C	G	T
01	0.146	0.002	0.03	0.821
02	0.079	0.005	0.891	0.025
03	0.938	0.005	0.012	0.045
04	0.027	0.069	0.057	0.846
05	0.184	0.007	0.03	0.779
06	0.365	0.025	0.581	0.03
07	0.928	0.042	0.025	0.005
08	0.042	0.02	0.089	0.849
09	0.082	0.06	0.521	0.337
10	0.308	0.084	0.494	0.114

PWM

	A	C	G	T
01	-0.525	-3.711	-2.025	1.179
02	-1.116	-3.375	1.26	-2.185
03	1.311	-3.375	-2.756	-1.657
04	-2.102	-1.243	-1.429	1.209
05	-0.303	-3.123	-2.025	1.127
06	0.373	-2.185	0.834	-2.025
07	1.301	-1.71	-2.185	-3.375
08	-1.71	-2.376	-1.003	1.212
09	-1.086	-1.389	0.727	0.296
10	0.205	-1.058	0.673	-0.767

Standard thresholds

P-value	Threshold
0.001	4.606935
0.0005	5.50509
0.0001	7.2635