PROP1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PROP1.H12INVITRO.0.PSM.A
Gene (human)	PROP1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Prop1
Gene synonyms (mouse)	Prop-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	16
Consensus	nvbTAATTRvRTTAvn
GC content	29.52%
Information content (bits; total / per base)	16.099 / 1.006
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9455

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
Mouse	1 (7)	0.925	0.934	0.853	0.88	0.897	0.91	3.592	3.669	367.824	415.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.999	0.997	0.996	0.994	0.975	0.972
Overall, 10 experiments	best	1.0	1.0	1.0	0.999	0.999	0.999
Methyl HT-SELEX, 3 experiments	median	0.999	0.999	0.999	0.998	0.989	0.987
Methyl HT-SELEX, 3 experiments	best	1.0	0.999	0.999	0.999	0.998	0.996
Non-Methyl HT-SELEX, 7 experiments	median	0.998	0.996	0.993	0.99	0.865	0.883
Non-Methyl HT-SELEX, 7 experiments	best	1.0	1.0	1.0	0.999	0.999	0.999

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.953	0.796	0.938	0.642
batch 2	0.866	0.626	0.839	0.655

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	PROP {3.1.3.20} (TFClass)
TFClass ID	TFClass: 3.1.3.20.1
HGNC	HGNC:9455
MGI	MGI:109330
EntrezGene (human)	GeneID:5626 (SSTAR profile)
EntrezGene (mouse)	GeneID:19127 (SSTAR profile)
UniProt ID (human)	PROP1_HUMAN
UniProt ID (mouse)	PROP1_MOUSE
UniProt AC (human)	O75360 (TFClass)
UniProt AC (mouse)	P97458 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	7
Methyl-HT-SELEX	3

PCM	PROP1.H12INVITRO.0.PSM.A.pcm
PWM	PROP1.H12INVITRO.0.PSM.A.pwm
PFM	PROP1.H12INVITRO.0.PSM.A.pfm
Alignment	PROP1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	PROP1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	PROP1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	PROP1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	PROP1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	PROP1.H12INVITRO.0.PSM.A_homer_format_0.001.txt PROP1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt PROP1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2120.25	2706.25	2649.25	1979.25
02	1934.0	2376.0	3820.0	1325.0
03	1051.0	3452.0	2361.0	2591.0
04	299.0	337.0	93.0	8726.0
05	9162.0	7.0	225.0	61.0
06	9453.0	0.0	2.0	0.0
07	8.0	47.0	21.0	9379.0
08	33.0	1770.0	336.0	7316.0
09	6252.0	18.0	2808.0	377.0
10	2503.0	2949.0	3901.0	102.0
11	6403.0	83.0	2803.0	166.0
12	4.0	7.0	8.0	9436.0
13	63.0	148.0	21.0	9223.0
14	8692.0	84.0	314.0	365.0
15	2843.5	1872.5	3539.5	1199.5
16	1413.0	3293.0	2602.0	2147.0

PFM

	A	C	G	T
01	0.224	0.286	0.28	0.209
02	0.205	0.251	0.404	0.14
03	0.111	0.365	0.25	0.274
04	0.032	0.036	0.01	0.923
05	0.969	0.001	0.024	0.006
06	1.0	0.0	0.0	0.0
07	0.001	0.005	0.002	0.992
08	0.003	0.187	0.036	0.774
09	0.661	0.002	0.297	0.04
10	0.265	0.312	0.413	0.011
11	0.677	0.009	0.296	0.018
12	0.0	0.001	0.001	0.998
13	0.007	0.016	0.002	0.975
14	0.919	0.009	0.033	0.039
15	0.301	0.198	0.374	0.127
16	0.149	0.348	0.275	0.227

PWM

	A	C	G	T
01	-0.109	0.135	0.114	-0.177
02	-0.2	0.005	0.48	-0.578
03	-0.809	0.378	-0.001	0.092
04	-2.061	-1.942	-3.212	1.305
05	1.354	-5.54	-2.343	-3.621
06	1.385	-6.941	-6.313	-6.941
07	-5.438	-3.871	-4.621	1.378
08	-4.205	-0.289	-1.945	1.129
09	0.972	-4.759	0.172	-1.831
10	0.057	0.221	0.501	-3.122
11	0.996	-3.323	0.17	-2.643
12	-5.93	-5.54	-5.438	1.384
13	-3.59	-2.756	-4.621	1.361
14	1.301	-3.311	-2.012	-1.863
15	0.185	-0.233	0.403	-0.677
16	-0.514	0.331	0.096	-0.096

Standard thresholds

P-value	Threshold
0.001	1.11351
0.0005	2.65276
0.0001	5.79856