HXA11.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA11.H12INVITRO.1.SM.B
Gene (human)	HOXA11 (GeneCards)
Gene synonyms (human)	HOX1I
Gene (mouse)	Hoxa11
Gene synonyms (mouse)	Hox-1.9, Hoxa-11
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	12
Consensus	ndTTTACGAYbh
GC content	37.38%
Information content (bits; total / per base)	12.474 / 1.04
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9350

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
Mouse	2 (14)	0.779	0.83	0.668	0.724	0.698	0.752	2.045	2.138	22.721	64.796

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.938	0.922	0.828	0.812	0.706	0.709
Overall, 4 experiments	best	0.989	0.986	0.899	0.893	0.755	0.767
Methyl HT-SELEX, 1 experiments	median	0.973	0.965	0.866	0.855	0.735	0.741
Methyl HT-SELEX, 1 experiments	best	0.973	0.965	0.866	0.855	0.735	0.741
Non-Methyl HT-SELEX, 3 experiments	median	0.903	0.879	0.791	0.769	0.677	0.677
Non-Methyl HT-SELEX, 3 experiments	best	0.989	0.986	0.899	0.893	0.755	0.767

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	HOX9-13 {3.1.1.8} (TFClass)
TFClass ID	TFClass: 3.1.1.8.9
HGNC	HGNC:5101
MGI	MGI:96172
EntrezGene (human)	GeneID:3207 (SSTAR profile)
EntrezGene (mouse)	GeneID:15396 (SSTAR profile)
UniProt ID (human)	HXA11_HUMAN
UniProt ID (mouse)	HXA11_MOUSE
UniProt AC (human)	P31270 (TFClass)
UniProt AC (mouse)	P31311 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	HXA11.H12INVITRO.1.SM.B.pcm
PWM	HXA11.H12INVITRO.1.SM.B.pwm
PFM	HXA11.H12INVITRO.1.SM.B.pfm
Alignment	HXA11.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	HXA11.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	HXA11.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	HXA11.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	HXA11.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	HXA11.H12INVITRO.1.SM.B_homer_format_0.001.txt HXA11.H12INVITRO.1.SM.B_homer_format_0.0005.txt HXA11.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3014.0	1780.0	2278.0	2278.0
02	1694.25	1160.25	1268.25	5227.25
03	405.0	236.0	474.0	8235.0
04	104.0	108.0	66.0	9072.0
05	1811.0	37.0	6.0	7496.0
06	9343.0	3.0	3.0	1.0
07	3.0	8489.0	3.0	855.0
08	32.0	32.0	9199.0	87.0
09	8772.0	194.0	233.0	151.0
10	141.0	5717.0	1179.0	2313.0
11	1385.75	4385.75	1754.75	1823.75
12	2173.0	1763.0	1571.0	3843.0

PFM

	A	C	G	T
01	0.322	0.19	0.244	0.244
02	0.181	0.124	0.136	0.559
03	0.043	0.025	0.051	0.881
04	0.011	0.012	0.007	0.97
05	0.194	0.004	0.001	0.802
06	0.999	0.0	0.0	0.0
07	0.0	0.908	0.0	0.091
08	0.003	0.003	0.984	0.009
09	0.938	0.021	0.025	0.016
10	0.015	0.611	0.126	0.247
11	0.148	0.469	0.188	0.195
12	0.232	0.189	0.168	0.411

PWM

	A	C	G	T
01	0.254	-0.272	-0.026	-0.026
02	-0.321	-0.699	-0.611	0.804
03	-1.748	-2.284	-1.592	1.259
04	-3.092	-3.055	-3.534	1.355
05	-0.255	-4.087	-5.643	1.165
06	1.385	-6.093	-6.093	-6.568
07	-6.093	1.289	-6.093	-1.004
08	-4.223	-4.223	1.369	-3.266
09	1.322	-2.478	-2.297	-2.726
10	-2.793	0.894	-0.683	-0.011
11	-0.522	0.629	-0.286	-0.248
12	-0.073	-0.282	-0.397	0.497

Standard thresholds

P-value	Threshold
0.001	3.684535
0.0005	4.88552
0.0001	7.233895