HXB13.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB13.H12INVITRO.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	12
Consensus	ndTTTACGAGvn
GC content	41.55%
Information content (bits; total / per base)	14.45 / 1.204
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7712

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)	0.785	0.855	0.646	0.751	0.708	0.769	1.981	2.471	45.551	165.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.967	0.958	0.919	0.904	0.837	0.83
Overall, 4 experiments	best	0.999	0.998	0.998	0.997	0.992	0.989
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.998	0.997	0.992	0.989
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.998	0.997	0.992	0.989
Non-Methyl HT-SELEX, 3 experiments	median	0.938	0.922	0.852	0.827	0.734	0.729
Non-Methyl HT-SELEX, 3 experiments	best	0.996	0.994	0.986	0.981	0.94	0.931

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.333	4.488	0.25	0.119

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.1.SM.B.pcm
PWM	HXB13.H12INVITRO.1.SM.B.pwm
PFM	HXB13.H12INVITRO.1.SM.B.pfm
Alignment	HXB13.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	HXB13.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	HXB13.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	HXB13.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	HXB13.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	HXB13.H12INVITRO.1.SM.B_homer_format_0.001.txt HXB13.H12INVITRO.1.SM.B_homer_format_0.0005.txt HXB13.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2070.25	1288.25	2795.25	1558.25
02	1417.0	608.0	2032.0	3655.0
03	85.0	24.0	132.0	7471.0
04	29.0	7.0	9.0	7667.0
05	447.0	3.0	1.0	7261.0
06	7712.0	0.0	0.0	0.0
07	0.0	7027.0	0.0	685.0
08	53.0	2.0	7603.0	54.0
09	7496.0	35.0	148.0	33.0
10	32.0	459.0	6859.0	362.0
11	1146.25	2585.25	3021.25	959.25
12	1573.75	1700.75	2107.75	2329.75

PFM

	A	C	G	T
01	0.268	0.167	0.362	0.202
02	0.184	0.079	0.263	0.474
03	0.011	0.003	0.017	0.969
04	0.004	0.001	0.001	0.994
05	0.058	0.0	0.0	0.942
06	1.0	0.0	0.0	0.0
07	0.0	0.911	0.0	0.089
08	0.007	0.0	0.986	0.007
09	0.972	0.005	0.019	0.004
10	0.004	0.06	0.889	0.047
11	0.149	0.335	0.392	0.124
12	0.204	0.221	0.273	0.302

PWM

	A	C	G	T
01	0.071	-0.403	0.371	-0.213
02	-0.308	-1.152	0.052	0.639
03	-3.097	-4.298	-2.666	1.354
04	-4.124	-5.342	-5.146	1.38
05	-1.458	-5.91	-6.391	1.325
06	1.385	-6.76	-6.76	-6.76
07	-6.76	1.292	-6.76	-1.033
08	-3.554	-6.121	1.371	-3.536
09	1.357	-3.948	-2.553	-4.003
10	-4.032	-1.431	1.268	-1.668
11	-0.519	0.293	0.449	-0.697
12	-0.203	-0.125	0.089	0.189

Standard thresholds

P-value	Threshold
0.001	1.99167
0.0005	3.449285
0.0001	6.483895