NKX25.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NKX25.H12INVIVO.0.PSM.A
Gene (human)	NKX2-5 (GeneCards)
Gene synonyms (human)	CSX, NKX2.5, NKX2E
Gene (mouse)	Nkx2-5
Gene synonyms (mouse)	Csx, Nkx-2.5, Nkx2e
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	nhKRAGWGbbh
GC content	50.76%
Information content (bits; total / per base)	7.986 / 0.726
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	989

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	2 (14)	0.856	0.865	0.726	0.741	0.742	0.753	1.944	2.003	166.214	196.276
Mouse	7 (29)	0.765	0.91	0.609	0.81	0.653	0.818	1.53	2.407	68.824	151.328

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.884	0.817	0.854	0.79	0.794	0.743
Overall, 2 experiments	best	0.898	0.835	0.873	0.811	0.819	0.767
Methyl HT-SELEX, 1 experiments	median	0.898	0.835	0.873	0.811	0.819	0.767
Methyl HT-SELEX, 1 experiments	best	0.898	0.835	0.873	0.811	0.819	0.767
Non-Methyl HT-SELEX, 1 experiments	median	0.869	0.798	0.835	0.768	0.769	0.72
Non-Methyl HT-SELEX, 1 experiments	best	0.869	0.798	0.835	0.768	0.769	0.72

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	NK4 {3.1.2.17} (TFClass)
TFClass ID	TFClass: 3.1.2.17.2
HGNC	HGNC:2488
MGI	MGI:97350
EntrezGene (human)	GeneID:1482 (SSTAR profile)
EntrezGene (mouse)	GeneID:18091 (SSTAR profile)
UniProt ID (human)	NKX25_HUMAN
UniProt ID (mouse)	NKX25_MOUSE
UniProt AC (human)	P52952 (TFClass)
UniProt AC (mouse)	P42582 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 7 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	NKX25.H12INVIVO.0.PSM.A.pcm
PWM	NKX25.H12INVIVO.0.PSM.A.pwm
PFM	NKX25.H12INVIVO.0.PSM.A.pfm
Alignment	NKX25.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	NKX25.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	NKX25.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	NKX25.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	NKX25.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	NKX25.H12INVIVO.0.PSM.A_homer_format_0.001.txt NKX25.H12INVIVO.0.PSM.A_homer_format_0.0005.txt NKX25.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	122.0	309.0	303.0	255.0
02	181.0	233.0	49.0	526.0
03	116.0	81.0	210.0	582.0
04	210.0	61.0	715.0	3.0
05	976.0	2.0	7.0	4.0
06	9.0	63.0	906.0	11.0
07	317.0	4.0	53.0	615.0
08	62.0	9.0	917.0	1.0
09	68.0	286.0	404.0	231.0
10	100.0	321.0	230.0	338.0
11	174.0	205.0	154.0	456.0

PFM

	A	C	G	T
01	0.123	0.312	0.306	0.258
02	0.183	0.236	0.05	0.532
03	0.117	0.082	0.212	0.588
04	0.212	0.062	0.723	0.003
05	0.987	0.002	0.007	0.004
06	0.009	0.064	0.916	0.011
07	0.321	0.004	0.054	0.622
08	0.063	0.009	0.927	0.001
09	0.069	0.289	0.408	0.234
10	0.101	0.325	0.233	0.342
11	0.176	0.207	0.156	0.461

PWM

	A	C	G	T
01	-0.699	0.222	0.202	0.031
02	-0.309	-0.059	-1.591	0.751
03	-0.749	-1.102	-0.162	0.852
04	-0.162	-1.379	1.057	-3.965
05	1.368	-4.203	-3.351	-3.773
06	-3.145	-1.347	1.294	-2.974
07	0.247	-3.773	-1.515	0.907
08	-1.363	-3.145	1.306	-4.515
09	-1.273	0.145	0.488	-0.067
10	-0.895	0.259	-0.072	0.311
11	-0.348	-0.186	-0.469	0.609

Standard thresholds

P-value	Threshold
0.001	5.238155
0.0005	5.898945
0.0001	7.10379