NKX31.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NKX31.H12INVIVO.0.PSM.A
Gene (human)	NKX3-1 (GeneCards)
Gene synonyms (human)	NKX3.1, NKX3A
Gene (mouse)	Nkx3-1
Gene synonyms (mouse)	Nkx-3.1, Nkx3a
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	nbdAAGTGbYW
GC content	40.8%
Information content (bits; total / per base)	9.558 / 0.869
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
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	3 (20)	0.713	0.78	0.551	0.624	0.66	0.723	1.678	1.964	61.724	120.921
Mouse	1 (5)	0.68	0.709	0.495	0.525	0.593	0.62	1.301	1.396	68.081	87.409

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.941	0.914	0.884	0.856	0.791	0.786
Overall, 6 experiments	best	0.986	0.977	0.98	0.966	0.964	0.947
Methyl HT-SELEX, 1 experiments	median	0.986	0.976	0.98	0.966	0.964	0.947
Methyl HT-SELEX, 1 experiments	best	0.986	0.976	0.98	0.966	0.964	0.947
Non-Methyl HT-SELEX, 5 experiments	median	0.914	0.879	0.812	0.784	0.691	0.689
Non-Methyl HT-SELEX, 5 experiments	best	0.986	0.977	0.971	0.957	0.931	0.9

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	NK-related {3.1.2} (TFClass)
TF subfamily	NK3 {3.1.2.16} (TFClass)
TFClass ID	TFClass: 3.1.2.16.1
HGNC	HGNC:7838
MGI	MGI:97352
EntrezGene (human)	GeneID:4824 (SSTAR profile)
EntrezGene (mouse)	GeneID:18095 (SSTAR profile)
UniProt ID (human)	NKX31_HUMAN
UniProt ID (mouse)	NKX31_MOUSE
UniProt AC (human)	Q99801 (TFClass)
UniProt AC (mouse)	P97436 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 1 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	NKX31.H12INVIVO.0.PSM.A.pcm
PWM	NKX31.H12INVIVO.0.PSM.A.pwm
PFM	NKX31.H12INVIVO.0.PSM.A.pfm
Alignment	NKX31.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	NKX31.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	NKX31.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	NKX31.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	NKX31.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	NKX31.H12INVIVO.0.PSM.A_homer_format_0.001.txt NKX31.H12INVIVO.0.PSM.A_homer_format_0.0005.txt NKX31.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	229.0	188.0	271.0	312.0
02	108.0	286.0	161.0	445.0
03	244.0	100.0	122.0	534.0
04	761.0	24.0	200.0	15.0
05	977.0	2.0	10.0	11.0
06	1.0	7.0	988.0	4.0
07	67.0	0.0	13.0	920.0
08	139.0	9.0	841.0	11.0
09	15.0	481.0	258.0	246.0
10	79.0	273.0	26.0	622.0
11	145.0	126.0	102.0	627.0

PFM

	A	C	G	T
01	0.229	0.188	0.271	0.312
02	0.108	0.286	0.161	0.445
03	0.244	0.1	0.122	0.534
04	0.761	0.024	0.2	0.015
05	0.977	0.002	0.01	0.011
06	0.001	0.007	0.988	0.004
07	0.067	0.0	0.013	0.92
08	0.139	0.009	0.841	0.011
09	0.015	0.481	0.258	0.246
10	0.079	0.273	0.026	0.622
11	0.145	0.126	0.102	0.627

PWM

	A	C	G	T
01	-0.087	-0.283	0.08	0.22
02	-0.83	0.134	-0.436	0.574
03	-0.024	-0.906	-0.71	0.755
04	1.109	-2.281	-0.221	-2.711
05	1.358	-4.213	-3.066	-2.985
06	-4.525	-3.362	1.369	-3.783
07	-1.298	-4.982	-2.839	1.298
08	-0.582	-3.156	1.208	-2.985
09	-2.711	0.651	0.031	-0.016
10	-1.137	0.087	-2.206	0.907
11	-0.54	-0.678	-0.887	0.915

Standard thresholds

P-value	Threshold
0.001	4.93265
0.0005	5.80288
0.0001	7.39905