HXB13.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB13.H12INVITRO.0.PS.A
Gene (human)	HOXB13 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Hoxb13
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nKTTTAYKRGbn
GC content	37.9%
Information content (bits; total / per base)	11.565 / 0.964
Data sources	ChIP-Seq + HT-SELEX
Aligned words	9981

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)	0.844	0.948	0.708	0.886	0.779	0.904	2.254	3.234	81.293	391.31

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.983	0.973	0.952	0.938	0.869	0.867
Overall, 4 experiments	best	0.997	0.995	0.993	0.99	0.984	0.978
Methyl HT-SELEX, 1 experiments	median	0.997	0.995	0.993	0.99	0.984	0.978
Methyl HT-SELEX, 1 experiments	best	0.997	0.995	0.993	0.99	0.984	0.978
Non-Methyl HT-SELEX, 3 experiments	median	0.972	0.958	0.918	0.897	0.77	0.777
Non-Methyl HT-SELEX, 3 experiments	best	0.993	0.988	0.987	0.98	0.969	0.957

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	20.559	8.796	0.325	0.215

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

PCM	HXB13.H12INVITRO.0.PS.A.pcm
PWM	HXB13.H12INVITRO.0.PS.A.pwm
PFM	HXB13.H12INVITRO.0.PS.A.pfm
Alignment	HXB13.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	HXB13.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	HXB13.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	HXB13.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	HXB13.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	HXB13.H12INVITRO.0.PS.A_homer_format_0.001.txt HXB13.H12INVITRO.0.PS.A_homer_format_0.0005.txt HXB13.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2121.5	1719.5	3482.5	2657.5
02	948.25	856.25	1983.25	6193.25
03	159.0	92.0	189.0	9541.0
04	164.0	33.0	34.0	9750.0
05	864.0	43.0	21.0	9053.0
06	9962.0	3.0	4.0	12.0
07	30.0	4886.0	1.0	5064.0
08	413.0	22.0	7173.0	2373.0
09	6285.0	75.0	3505.0	116.0
10	263.0	1037.0	8147.0	534.0
11	1379.5	3284.5	3560.5	1756.5
12	1598.25	2819.25	2423.25	3140.25

PFM

	A	C	G	T
01	0.213	0.172	0.349	0.266
02	0.095	0.086	0.199	0.621
03	0.016	0.009	0.019	0.956
04	0.016	0.003	0.003	0.977
05	0.087	0.004	0.002	0.907
06	0.998	0.0	0.0	0.001
07	0.003	0.49	0.0	0.507
08	0.041	0.002	0.719	0.238
09	0.63	0.008	0.351	0.012
10	0.026	0.104	0.816	0.054
11	0.138	0.329	0.357	0.176
12	0.16	0.282	0.243	0.315

PWM

	A	C	G	T
01	-0.162	-0.372	0.333	0.063
02	-0.966	-1.068	-0.229	0.909
03	-2.74	-3.277	-2.569	1.341
04	-2.709	-4.259	-4.231	1.362
05	-1.059	-4.01	-4.675	1.288
06	1.384	-6.155	-5.982	-5.163
07	-4.348	0.672	-6.629	0.707
08	-1.794	-4.633	1.055	-0.05
09	0.923	-3.475	0.34	-3.05
10	-2.242	-0.877	1.183	-1.538
11	-0.592	0.275	0.355	-0.351
12	-0.445	0.122	-0.029	0.23

Standard thresholds

P-value	Threshold
0.001	4.09236
0.0005	5.217065
0.0001	7.48429