PDX1.H12INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PDX1.H12INVITRO.1.PSM.A
Gene (human)	PDX1 (GeneCards)
Gene synonyms (human)	IPF1, STF1
Gene (mouse)	Pdx1
Gene synonyms (mouse)	Ipf1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	13
Consensus	nvvYTAATKRbnn
GC content	38.84%
Information content (bits; total / per base)	11.138 / 0.857
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8990

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)	0.623	0.643	0.469	0.497	0.576	0.593	1.34	1.418	39.114	61.31
Mouse	4 (26)	0.646	0.91	0.473	0.84	0.532	0.852	1.197	2.511	27.665	125.481

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.973	0.957	0.929	0.91	0.834	0.831
Overall, 4 experiments	best	0.984	0.973	0.974	0.959	0.957	0.936
Methyl HT-SELEX, 1 experiments	median	0.984	0.973	0.974	0.959	0.957	0.936
Methyl HT-SELEX, 1 experiments	best	0.984	0.973	0.974	0.959	0.957	0.936
Non-Methyl HT-SELEX, 3 experiments	median	0.967	0.952	0.891	0.873	0.724	0.743
Non-Methyl HT-SELEX, 3 experiments	best	0.978	0.963	0.967	0.947	0.945	0.92

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.852	0.589	0.849	0.632

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.1.PSM.A.pcm
PWM	PDX1.H12INVITRO.1.PSM.A.pwm
PFM	PDX1.H12INVITRO.1.PSM.A.pfm
Alignment	PDX1.H12INVITRO.1.PSM.A.words.tsv
Threshold to P-value map	PDX1.H12INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	PDX1.H12INVITRO.1.PSM.A_jaspar_format.txt
MEME format	PDX1.H12INVITRO.1.PSM.A_meme_format.meme
Transfac format	PDX1.H12INVITRO.1.PSM.A_transfac_format.txt
Homer format	PDX1.H12INVITRO.1.PSM.A_homer_format_0.001.txt PDX1.H12INVITRO.1.PSM.A_homer_format_0.0005.txt PDX1.H12INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2223.0	2189.0	2419.0	2159.0
02	1745.75	3677.75	2125.75	1440.75
03	2467.0	2402.0	3661.0	460.0
04	94.0	4747.0	773.0	3376.0
05	0.0	0.0	0.0	8990.0
06	8990.0	0.0	0.0	0.0
07	8990.0	0.0	0.0	0.0
08	0.0	2.0	0.0	8988.0
09	1.0	175.0	4108.0	4706.0
10	6567.0	92.0	2152.0	179.0
11	632.0	4211.0	2667.0	1480.0
12	1555.5	2897.5	2719.5	1817.5
13	2355.25	2424.25	1950.25	2260.25

PFM

	A	C	G	T
01	0.247	0.243	0.269	0.24
02	0.194	0.409	0.236	0.16
03	0.274	0.267	0.407	0.051
04	0.01	0.528	0.086	0.376
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.019	0.457	0.523
10	0.73	0.01	0.239	0.02
11	0.07	0.468	0.297	0.165
12	0.173	0.322	0.303	0.202
13	0.262	0.27	0.217	0.251

PWM

	A	C	G	T
01	-0.011	-0.026	0.073	-0.04
02	-0.252	0.492	-0.056	-0.444
03	0.093	0.066	0.488	-1.582
04	-3.151	0.747	-1.065	0.407
05	-6.896	-6.896	-6.896	1.386
06	1.386	-6.896	-6.896	-6.896
07	1.386	-6.896	-6.896	-6.896
08	-6.896	-6.266	-6.896	1.385
09	-6.532	-2.541	0.603	0.738
10	1.072	-3.172	-0.043	-2.519
11	-1.266	0.627	0.171	-0.417
12	-0.368	0.254	0.19	-0.212
13	0.047	0.076	-0.142	0.006

Standard thresholds

P-value	Threshold
0.001	3.99901
0.0005	5.61196
0.0001	7.88571