HXB13.H13RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB13.H13RSNP.1.SM.B
Gene (human)	HOXB13 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Hoxb13
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	13
Consensus	nnKTTTACGAGbn
GC content	41.92%
Information content (bits; total / per base)	15.798 / 1.215
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	308
Previous names	HXB13.H12RSNP.1.SM.B

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	21 (108)	0.662	0.711	0.563	0.644	0.689	0.757	1.91	2.428	37.988	165.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.965	0.956	0.914	0.898	0.823	0.819
Overall, 4 experiments	best	0.999	0.998	0.997	0.995	0.988	0.985
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.997	0.995	0.988	0.985
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.997	0.995	0.988	0.985
Non-Methyl HT-SELEX, 3 experiments	median	0.934	0.919	0.842	0.816	0.714	0.714
Non-Methyl HT-SELEX, 3 experiments	best	0.996	0.993	0.986	0.98	0.933	0.923

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	6.11	4.473	0.252	0.12

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: 3.1.1.8.15
HGNC	HGNC:5112
MGI	MGI:107730
EntrezGene (human)	GeneID:10481 (SSTAR profile)
EntrezGene (mouse)	GeneID:15408 (SSTAR profile)
UniProt ID (human)	HXB13_HUMAN
UniProt ID (mouse)	HXB13_MOUSE
UniProt AC (human)	Q92826 (TFClass)
UniProt AC (mouse)	P70321 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	21 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	HXB13.H13RSNP.1.SM.B.pcm
PWM	HXB13.H13RSNP.1.SM.B.pwm
PFM	HXB13.H13RSNP.1.SM.B.pfm
Threshold to P-value map	HXB13.H13RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	HXB13.H13RSNP.1.SM.B_jaspar_format.txt
MEME format	HXB13.H13RSNP.1.SM.B_meme_format.meme
Transfac format	HXB13.H13RSNP.1.SM.B_transfac_format.txt
Homer format	HXB13.H13RSNP.1.SM.B_homer_format_0.001.txt HXB13.H13RSNP.1.SM.B_homer_format_0.0005.txt HXB13.H13RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	61.75	85.75	73.75	86.75
02	75.0	59.0	99.0	75.0
03	21.0	26.0	67.0	194.0
04	0.0	1.0	0.0	307.0
05	0.0	0.0	0.0	308.0
06	3.0	0.0	0.0	305.0
07	308.0	0.0	0.0	0.0
08	0.0	239.0	0.0	69.0
09	0.0	0.0	308.0	0.0
10	304.0	0.0	4.0	0.0
11	0.0	2.0	305.0	1.0
12	34.5	103.5	123.5	46.5
13	29.5	85.5	96.5	96.5

PFM

	A	C	G	T
01	0.2	0.278	0.239	0.282
02	0.244	0.192	0.321	0.244
03	0.068	0.084	0.218	0.63
04	0.0	0.003	0.0	0.997
05	0.0	0.0	0.0	1.0
06	0.01	0.0	0.0	0.99
07	1.0	0.0	0.0	0.0
08	0.0	0.776	0.0	0.224
09	0.0	0.0	1.0	0.0
10	0.987	0.0	0.013	0.0
11	0.0	0.006	0.99	0.003
12	0.112	0.336	0.401	0.151
13	0.096	0.278	0.313	0.313

PWM

	A	C	G	T
01	-0.216	0.106	-0.042	0.117
02	-0.026	-0.261	0.247	-0.026
03	-1.252	-1.051	-0.136	0.913
04	-4.003	-3.473	-4.003	1.369
05	-4.003	-4.003	-4.003	1.373
06	-2.873	-4.003	-4.003	1.363
07	1.373	-4.003	-4.003	-4.003
08	-4.003	1.12	-4.003	-0.108
09	-4.003	-4.003	1.373	-4.003
10	1.359	-4.003	-2.67	-4.003
11	-4.003	-3.129	1.363	-3.473
12	-0.781	0.291	0.466	-0.492
13	-0.93	0.103	0.222	0.222

Standard thresholds

P-value	Threshold
0.001	1.602055
0.0005	3.557675
0.0001	6.040555