PDX1.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PDX1.H12INVITRO.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	TGATWRATKR
GC content	30.47%
Information content (bits; total / per base)	11.197 / 1.12
Data sources	ChIP-Seq
Aligned words	971

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)	0.924	0.958	0.872	0.924	0.905	0.943	3.569	4.101	478.495	639.921
Mouse	4 (26)	0.805	0.933	0.677	0.901	0.733	0.905	2.223	3.874	44.62	384.585

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.732	0.665	0.695	0.638	0.649	0.609
Overall, 4 experiments	best	0.778	0.704	0.74	0.674	0.7	0.646
Methyl HT-SELEX, 1 experiments	median	0.778	0.704	0.74	0.674	0.7	0.646
Methyl HT-SELEX, 1 experiments	best	0.778	0.704	0.74	0.674	0.7	0.646
Non-Methyl HT-SELEX, 3 experiments	median	0.709	0.646	0.664	0.615	0.61	0.584
Non-Methyl HT-SELEX, 3 experiments	best	0.755	0.684	0.726	0.66	0.687	0.634

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.616	0.119	0.645	0.431

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.H12INVITRO.0.P.B.pcm
PWM	PDX1.H12INVITRO.0.P.B.pwm
PFM	PDX1.H12INVITRO.0.P.B.pfm
Alignment	PDX1.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	PDX1.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	PDX1.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	PDX1.H12INVITRO.0.P.B_meme_format.meme
Transfac format	PDX1.H12INVITRO.0.P.B_transfac_format.txt
Homer format	PDX1.H12INVITRO.0.P.B_homer_format_0.001.txt PDX1.H12INVITRO.0.P.B_homer_format_0.0005.txt PDX1.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	172.0	2.0	23.0	774.0
02	39.0	7.0	913.0	12.0
03	921.0	22.0	8.0	20.0
04	18.0	96.0	35.0	822.0
05	183.0	7.0	57.0	724.0
06	455.0	13.0	487.0	16.0
07	919.0	14.0	24.0	14.0
08	35.0	35.0	70.0	831.0
09	62.0	41.0	596.0	272.0
10	375.0	38.0	471.0	87.0

PFM

	A	C	G	T
01	0.177	0.002	0.024	0.797
02	0.04	0.007	0.94	0.012
03	0.949	0.023	0.008	0.021
04	0.019	0.099	0.036	0.847
05	0.188	0.007	0.059	0.746
06	0.469	0.013	0.502	0.016
07	0.946	0.014	0.025	0.014
08	0.036	0.036	0.072	0.856
09	0.064	0.042	0.614	0.28
10	0.386	0.039	0.485	0.09

PWM

	A	C	G	T
01	-0.342	-4.185	-2.291	1.155
02	-1.792	-3.334	1.32	-2.88
03	1.328	-2.333	-3.225	-2.421
04	-2.517	-0.917	-1.896	1.215
05	-0.28	-3.334	-1.426	1.088
06	0.625	-2.81	0.693	-2.624
07	1.326	-2.744	-2.252	-2.744
08	-1.896	-1.896	-1.226	1.226
09	-1.345	-1.744	0.894	0.113
10	0.432	-1.817	0.659	-1.014

Standard thresholds

P-value	Threshold
0.001	4.41324
0.0005	5.323135
0.0001	7.18506