NKX25.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NKX25.H12INVITRO.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	10
Consensus	bWYAAGTGSn
GC content	46.49%
Information content (bits; total / per base)	10.995 / 1.1
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9953

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)	0.754	0.763	0.6	0.618	0.706	0.716	1.802	1.86	90.651	104.215
Mouse	7 (29)	0.741	0.807	0.596	0.651	0.697	0.749	1.807	1.944	54.081	122.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.983	0.971	0.961	0.946	0.883	0.87
Overall, 2 experiments	best	0.992	0.985	0.985	0.977	0.917	0.91
Methyl HT-SELEX, 1 experiments	median	0.992	0.985	0.985	0.977	0.917	0.91
Methyl HT-SELEX, 1 experiments	best	0.992	0.985	0.985	0.977	0.917	0.91
Non-Methyl HT-SELEX, 1 experiments	median	0.974	0.957	0.937	0.914	0.848	0.83
Non-Methyl HT-SELEX, 1 experiments	best	0.974	0.957	0.937	0.914	0.848	0.83

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.H12INVITRO.0.PSM.A.pcm
PWM	NKX25.H12INVITRO.0.PSM.A.pwm
PFM	NKX25.H12INVITRO.0.PSM.A.pfm
Alignment	NKX25.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	NKX25.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	NKX25.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	NKX25.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	NKX25.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	NKX25.H12INVITRO.0.PSM.A_homer_format_0.001.txt NKX25.H12INVITRO.0.PSM.A_homer_format_0.0005.txt NKX25.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1331.75	3350.75	3286.75	1983.75
02	1575.5	1039.5	1159.5	6178.5
03	280.0	3296.0	859.0	5518.0
04	9673.0	0.0	278.0	2.0
05	9953.0	0.0	0.0	0.0
06	0.0	0.0	9953.0	0.0
07	81.0	1.0	17.0	9854.0
08	595.0	4.0	9351.0	3.0
09	302.0	3009.0	5521.0	1121.0
10	1932.5	2668.5	2477.5	2874.5

PFM

	A	C	G	T
01	0.134	0.337	0.33	0.199
02	0.158	0.104	0.116	0.621
03	0.028	0.331	0.086	0.554
04	0.972	0.0	0.028	0.0
05	1.0	0.0	0.0	0.0
06	0.0	0.0	1.0	0.0
07	0.008	0.0	0.002	0.99
08	0.06	0.0	0.94	0.0
09	0.03	0.302	0.555	0.113
10	0.194	0.268	0.249	0.289

PWM

	A	C	G	T
01	-0.624	0.297	0.278	-0.226
02	-0.456	-0.872	-0.763	0.909
03	-2.177	0.281	-1.062	0.796
04	1.357	-6.987	-2.184	-6.361
05	1.386	-6.987	-6.987	-6.987
06	-6.987	-6.987	1.386	-6.987
07	-3.398	-6.626	-4.86	1.376
08	-1.428	-5.979	1.323	-6.152
09	-2.102	0.19	0.796	-0.796
10	-0.252	0.07	-0.004	0.144

Standard thresholds

P-value	Threshold
0.001	4.345585
0.0005	5.67194
0.0001	7.72607