NKX31.H12RSNP.0.PSM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NKX31.H12RSNP.0.PSM.D
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	D

Motif length	14
Consensus	nYTAAGTGSbhhhh
GC content	41.87%
Information content (bits; total / per base)	13.218 / 0.944
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9937

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)	0.695	0.772	0.513	0.62	0.614	0.687	1.404	1.718	39.689	101.886
Mouse	1 (5)	0.671	0.688	0.481	0.497	0.556	0.572	1.194	1.248	43.523	63.585

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.97	0.957	0.909	0.895	0.812	0.815
Overall, 6 experiments	best	0.998	0.996	0.989	0.986	0.977	0.967
Methyl HT-SELEX, 1 experiments	median	0.992	0.987	0.988	0.981	0.977	0.967
Methyl HT-SELEX, 1 experiments	best	0.992	0.987	0.988	0.981	0.977	0.967
Non-Methyl HT-SELEX, 5 experiments	median	0.953	0.938	0.841	0.826	0.71	0.717
Non-Methyl HT-SELEX, 5 experiments	best	0.998	0.996	0.989	0.986	0.954	0.935

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.H12RSNP.0.PSM.D.pcm
PWM	NKX31.H12RSNP.0.PSM.D.pwm
PFM	NKX31.H12RSNP.0.PSM.D.pfm
Alignment	NKX31.H12RSNP.0.PSM.D.words.tsv
Threshold to P-value map	NKX31.H12RSNP.0.PSM.D.thr
Motif in other formats
JASPAR format	NKX31.H12RSNP.0.PSM.D_jaspar_format.txt
MEME format	NKX31.H12RSNP.0.PSM.D_meme_format.meme
Transfac format	NKX31.H12RSNP.0.PSM.D_transfac_format.txt
Homer format	NKX31.H12RSNP.0.PSM.D_homer_format_0.001.txt NKX31.H12RSNP.0.PSM.D_homer_format_0.0005.txt NKX31.H12RSNP.0.PSM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1944.0	3192.0	2469.0	2332.0
02	1310.25	1373.25	949.25	6304.25
03	161.0	139.0	266.0	9371.0
04	9769.0	0.0	159.0	9.0
05	9933.0	3.0	0.0	1.0
06	8.0	0.0	9912.0	17.0
07	21.0	18.0	15.0	9883.0
08	899.0	6.0	9017.0	15.0
09	173.0	2681.0	6556.0	527.0
10	1094.0	3655.0	1472.0	3716.0
11	3554.0	2453.0	896.0	3034.0
12	2511.0	5075.0	872.0	1479.0
13	1623.0	3082.0	979.0	4253.0
14	1894.25	1821.25	1190.25	5031.25

PFM

	A	C	G	T
01	0.196	0.321	0.248	0.235
02	0.132	0.138	0.096	0.634
03	0.016	0.014	0.027	0.943
04	0.983	0.0	0.016	0.001
05	1.0	0.0	0.0	0.0
06	0.001	0.0	0.997	0.002
07	0.002	0.002	0.002	0.995
08	0.09	0.001	0.907	0.002
09	0.017	0.27	0.66	0.053
10	0.11	0.368	0.148	0.374
11	0.358	0.247	0.09	0.305
12	0.253	0.511	0.088	0.149
13	0.163	0.31	0.099	0.428
14	0.191	0.183	0.12	0.506

PWM

	A	C	G	T
01	-0.245	0.25	-0.006	-0.063
02	-0.639	-0.592	-0.961	0.931
03	-2.723	-2.868	-2.227	1.327
04	1.369	-6.985	-2.735	-5.394
05	1.385	-6.151	-6.985	-6.624
06	-5.486	-6.985	1.383	-4.858
07	-4.67	-4.808	-4.968	1.38
08	-1.015	-5.702	1.288	-4.968
09	-2.652	0.076	0.97	-1.547
10	-0.819	0.386	-0.523	0.402
11	0.358	-0.013	-1.018	0.2
12	0.011	0.714	-1.045	-0.518
13	-0.425	0.215	-0.93	0.537
14	-0.271	-0.31	-0.735	0.705

Standard thresholds

P-value	Threshold
0.001	2.91571
0.0005	4.33296
0.0001	7.19646