HXA4.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA4.H12INVITRO.0.SM.B
Gene (human)	HOXA4 (GeneCards)
Gene synonyms (human)	HOX1D
Gene (mouse)	Hoxa4
Gene synonyms (mouse)	Hox-1.4, Hoxa-4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	12
Consensus	nnvYTAATKRbn
GC content	36.78%
Information content (bits; total / per base)	10.328 / 0.861
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9562

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.953	0.923	0.93	0.894	0.863	0.832
Overall, 2 experiments	best	0.957	0.93	0.933	0.9	0.869	0.833
Methyl HT-SELEX, 1 experiments	median	0.957	0.93	0.933	0.9	0.858	0.831
Methyl HT-SELEX, 1 experiments	best	0.957	0.93	0.933	0.9	0.858	0.831
Non-Methyl HT-SELEX, 1 experiments	median	0.949	0.917	0.927	0.888	0.869	0.833
Non-Methyl HT-SELEX, 1 experiments	best	0.949	0.917	0.927	0.888	0.869	0.833

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HOX-related {3.1.1} (TFClass)
TF subfamily	HOX4 {3.1.1.4} (TFClass)
TFClass ID	TFClass: 3.1.1.4.1
HGNC	HGNC:5105
MGI	MGI:96176
EntrezGene (human)	GeneID:3201 (SSTAR profile)
EntrezGene (mouse)	GeneID:15401 (SSTAR profile)
UniProt ID (human)	HXA4_HUMAN
UniProt ID (mouse)	HXA4_MOUSE
UniProt AC (human)	Q00056 (TFClass)
UniProt AC (mouse)	P06798 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXA4.H12INVITRO.0.SM.B.pcm
PWM	HXA4.H12INVITRO.0.SM.B.pwm
PFM	HXA4.H12INVITRO.0.SM.B.pfm
Alignment	HXA4.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	HXA4.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	HXA4.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	HXA4.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	HXA4.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	HXA4.H12INVITRO.0.SM.B_homer_format_0.001.txt HXA4.H12INVITRO.0.SM.B_homer_format_0.0005.txt HXA4.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2585.0	2337.0	2497.0	2143.0
02	1992.0	3814.0	1989.0	1767.0
03	2371.0	2436.0	4179.0	576.0
04	439.0	3497.0	951.0	4675.0
05	10.0	13.0	0.0	9539.0
06	9562.0	0.0	0.0	0.0
07	9562.0	0.0	0.0	0.0
08	0.0	926.0	1.0	8635.0
09	10.0	106.0	6180.0	3266.0
10	7011.0	163.0	2130.0	258.0
11	1102.75	3193.75	2074.75	3190.75
12	1606.0	2922.0	2799.0	2235.0

PFM

	A	C	G	T
01	0.27	0.244	0.261	0.224
02	0.208	0.399	0.208	0.185
03	0.248	0.255	0.437	0.06
04	0.046	0.366	0.099	0.489
05	0.001	0.001	0.0	0.998
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.097	0.0	0.903
09	0.001	0.011	0.646	0.342
10	0.733	0.017	0.223	0.027
11	0.115	0.334	0.217	0.334
12	0.168	0.306	0.293	0.234

PWM

	A	C	G	T
01	0.078	-0.023	0.044	-0.109
02	-0.182	0.467	-0.184	-0.302
03	-0.008	0.019	0.558	-1.42
04	-1.691	0.38	-0.92	0.67
05	-5.271	-5.053	-6.951	1.383
06	1.386	-6.951	-6.951	-6.951
07	1.386	-6.951	-6.951	-6.951
08	-6.951	-0.947	-6.589	1.284
09	-5.271	-3.095	0.949	0.312
10	1.075	-2.673	-0.115	-2.218
11	-0.773	0.289	-0.142	0.289
12	-0.397	0.201	0.158	-0.067

Standard thresholds

P-value	Threshold
0.001	4.84506
0.0005	5.981265
0.0001	7.728405