HXC10.H12INVITRO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC10.H12INVITRO.2.SM.B
Gene (human)	HOXC10 (GeneCards)
Gene synonyms (human)	HOX3I
Gene (mouse)	Hoxc10
Gene synonyms (mouse)	Hox-3.6, Hoxc-10
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	12
Consensus	ndTTTACGAYbn
GC content	38.07%
Information content (bits; total / per base)	12.726 / 1.06
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	1962

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 (10)	0.629	0.675	0.476	0.527	0.604	0.661	1.496	1.716	15.608	26.276

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.957	0.94	0.91	0.883	0.829	0.806
Overall, 8 experiments	best	0.999	0.998	0.997	0.996	0.98	0.976
Methyl HT-SELEX, 2 experiments	median	0.998	0.996	0.995	0.992	0.969	0.963
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.997	0.996	0.98	0.976
Non-Methyl HT-SELEX, 6 experiments	median	0.889	0.853	0.834	0.79	0.747	0.719
Non-Methyl HT-SELEX, 6 experiments	best	0.996	0.994	0.989	0.985	0.953	0.943

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: 3.1.1.8.7
HGNC	HGNC:5122
MGI	MGI:96192
EntrezGene (human)	GeneID:3226 (SSTAR profile)
EntrezGene (mouse)	GeneID:209448 (SSTAR profile)
UniProt ID (human)	HXC10_HUMAN
UniProt ID (mouse)	HXC10_MOUSE
UniProt AC (human)	Q9NYD6 (TFClass)
UniProt AC (mouse)	P31257 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	HXC10.H12INVITRO.2.SM.B.pcm
PWM	HXC10.H12INVITRO.2.SM.B.pwm
PFM	HXC10.H12INVITRO.2.SM.B.pfm
Alignment	HXC10.H12INVITRO.2.SM.B.words.tsv
Threshold to P-value map	HXC10.H12INVITRO.2.SM.B.thr
Motif in other formats
JASPAR format	HXC10.H12INVITRO.2.SM.B_jaspar_format.txt
MEME format	HXC10.H12INVITRO.2.SM.B_meme_format.meme
Transfac format	HXC10.H12INVITRO.2.SM.B_transfac_format.txt
Homer format	HXC10.H12INVITRO.2.SM.B_homer_format_0.001.txt HXC10.H12INVITRO.2.SM.B_homer_format_0.0005.txt HXC10.H12INVITRO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	484.0	515.0	557.0	406.0
02	419.5	254.5	365.5	922.5
03	128.0	4.0	33.0	1797.0
04	0.0	0.0	1.0	1961.0
05	383.0	0.0	0.0	1579.0
06	1962.0	0.0	0.0	0.0
07	0.0	1557.0	0.0	405.0
08	0.0	2.0	1937.0	23.0
09	1906.0	12.0	32.0	12.0
10	3.0	1122.0	287.0	550.0
11	269.0	906.0	509.0	278.0
12	467.0	469.0	400.0	626.0

PFM

	A	C	G	T
01	0.247	0.262	0.284	0.207
02	0.214	0.13	0.186	0.47
03	0.065	0.002	0.017	0.916
04	0.0	0.0	0.001	0.999
05	0.195	0.0	0.0	0.805
06	1.0	0.0	0.0	0.0
07	0.0	0.794	0.0	0.206
08	0.0	0.001	0.987	0.012
09	0.971	0.006	0.016	0.006
10	0.002	0.572	0.146	0.28
11	0.137	0.462	0.259	0.142
12	0.238	0.239	0.204	0.319

PWM

	A	C	G	T
01	-0.013	0.049	0.127	-0.188
02	-0.156	-0.653	-0.293	0.63
03	-1.333	-4.425	-2.647	1.296
04	-5.56	-5.56	-5.136	1.383
05	-0.246	-5.56	-5.56	1.166
06	1.383	-5.56	-5.56	-5.56
07	-5.56	1.152	-5.56	-0.191
08	-5.56	-4.839	1.371	-2.985
09	1.354	-3.568	-2.676	-3.568
10	-4.611	0.825	-0.533	0.114
11	-0.598	0.612	0.037	-0.565
12	-0.049	-0.045	-0.203	0.243

Standard thresholds

P-value	Threshold
0.001	3.118825
0.0005	4.39491
0.0001	7.539075