HMX1.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HMX1.H12RSNP.0.SM.B
Gene (human)	HMX1 (GeneCards)
Gene synonyms (human)	H6
Gene (mouse)	Hmx1
Gene synonyms (mouse)	H6
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	nTTAATTGnhn
GC content	28.89%
Information content (bits; total / per base)	12.954 / 1.178
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	1435

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.839	0.795	0.777	0.743	0.712	0.693
Overall, 4 experiments	best	0.939	0.896	0.908	0.862	0.853	0.807
Methyl HT-SELEX, 1 experiments	median	0.939	0.896	0.908	0.862	0.843	0.804
Methyl HT-SELEX, 1 experiments	best	0.939	0.896	0.908	0.862	0.843	0.804
Non-Methyl HT-SELEX, 3 experiments	median	0.754	0.711	0.65	0.633	0.581	0.583
Non-Methyl HT-SELEX, 3 experiments	best	0.925	0.879	0.903	0.853	0.853	0.807

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.784	0.556	0.801	0.602

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	NK5-HMX {3.1.2.18} (TFClass)
TFClass ID	TFClass: 3.1.2.18.1
HGNC	HGNC:5017
MGI	MGI:107178
EntrezGene (human)	GeneID:3166 (SSTAR profile)
EntrezGene (mouse)	GeneID:15371 (SSTAR profile)
UniProt ID (human)	HMX1_HUMAN
UniProt ID (mouse)	HMX1_MOUSE
UniProt AC (human)	Q9NP08 (TFClass)
UniProt AC (mouse)	O70218 (TFClass)
GRECO-DB-TF	yes

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

PCM	HMX1.H12RSNP.0.SM.B.pcm
PWM	HMX1.H12RSNP.0.SM.B.pwm
PFM	HMX1.H12RSNP.0.SM.B.pfm
Alignment	HMX1.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	HMX1.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	HMX1.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	HMX1.H12RSNP.0.SM.B_meme_format.meme
Transfac format	HMX1.H12RSNP.0.SM.B_transfac_format.txt
Homer format	HMX1.H12RSNP.0.SM.B_homer_format_0.001.txt HMX1.H12RSNP.0.SM.B_homer_format_0.0005.txt HMX1.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	491.0	307.0	287.0	350.0
02	10.0	21.0	7.0	1397.0
03	0.0	12.0	0.0	1423.0
04	1435.0	0.0	0.0	0.0
05	1435.0	0.0	0.0	0.0
06	0.0	0.0	510.0	925.0
07	0.0	32.0	0.0	1403.0
08	0.0	0.0	1435.0	0.0
09	309.0	505.0	305.0	316.0
10	206.25	368.25	194.25	666.25
11	324.75	356.75	219.75	533.75

PFM

	A	C	G	T
01	0.342	0.214	0.2	0.244
02	0.007	0.015	0.005	0.974
03	0.0	0.008	0.0	0.992
04	1.0	0.0	0.0	0.0
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.355	0.645
07	0.0	0.022	0.0	0.978
08	0.0	0.0	1.0	0.0
09	0.215	0.352	0.213	0.22
10	0.144	0.257	0.135	0.464
11	0.226	0.249	0.153	0.372

PWM

	A	C	G	T
01	0.312	-0.155	-0.222	-0.025
02	-3.418	-2.76	-3.711	1.356
03	-5.29	-3.262	-5.29	1.374
04	1.383	-5.29	-5.29	-5.29
05	1.383	-5.29	-5.29	-5.29
06	-5.29	-5.29	0.35	0.944
07	-5.29	-2.367	-5.29	1.36
08	-5.29	-5.29	1.383	-5.29
09	-0.148	0.34	-0.161	-0.126
10	-0.55	0.026	-0.609	0.617
11	-0.099	-0.006	-0.487	0.396

Standard thresholds

P-value	Threshold
0.001	2.75337
0.0005	3.940975
0.0001	7.985955