HXB13.H12RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB13.H12RSNP.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	10
Consensus	YTTTATdRvn
GC content	28.26%
Information content (bits; total / per base)	10.505 / 1.05
Data sources	ChIP-Seq + HT-SELEX
Aligned words	500

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)	0.838	0.945	0.72	0.895	0.796	0.908	2.293	3.319	83.382	433.284

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.951	0.927	0.908	0.876	0.824	0.805
Overall, 4 experiments	best	0.983	0.973	0.966	0.949	0.928	0.906
Methyl HT-SELEX, 1 experiments	median	0.947	0.92	0.926	0.887	0.906	0.862
Methyl HT-SELEX, 1 experiments	best	0.947	0.92	0.926	0.887	0.906	0.862
Non-Methyl HT-SELEX, 3 experiments	median	0.955	0.935	0.89	0.865	0.742	0.748
Non-Methyl HT-SELEX, 3 experiments	best	0.983	0.973	0.966	0.949	0.928	0.906

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	22.546	9.47	0.302	0.279

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.H12RSNP.0.PS.A.pcm
PWM	HXB13.H12RSNP.0.PS.A.pwm
PFM	HXB13.H12RSNP.0.PS.A.pfm
Alignment	HXB13.H12RSNP.0.PS.A.words.tsv
Threshold to P-value map	HXB13.H12RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	HXB13.H12RSNP.0.PS.A_jaspar_format.txt
MEME format	HXB13.H12RSNP.0.PS.A_meme_format.meme
Transfac format	HXB13.H12RSNP.0.PS.A_transfac_format.txt
Homer format	HXB13.H12RSNP.0.PS.A_homer_format_0.001.txt HXB13.H12RSNP.0.PS.A_homer_format_0.0005.txt HXB13.H12RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	34.0	54.0	50.0	362.0
02	5.0	3.0	9.0	483.0
03	0.0	2.0	1.0	497.0
04	7.0	12.0	13.0	468.0
05	472.0	11.0	17.0	0.0
06	12.0	50.0	1.0	437.0
07	131.0	5.0	162.0	202.0
08	125.0	4.0	328.0	43.0
09	51.0	165.0	250.0	34.0
10	96.0	192.0	84.0	128.0

PFM

	A	C	G	T
01	0.068	0.108	0.1	0.724
02	0.01	0.006	0.018	0.966
03	0.0	0.004	0.002	0.994
04	0.014	0.024	0.026	0.936
05	0.944	0.022	0.034	0.0
06	0.024	0.1	0.002	0.874
07	0.262	0.01	0.324	0.404
08	0.25	0.008	0.656	0.086
09	0.102	0.33	0.5	0.068
10	0.192	0.384	0.168	0.256

PWM

	A	C	G	T
01	-1.27	-0.823	-0.898	1.055
02	-2.961	-3.325	-2.484	1.343
03	-4.4	-3.573	-3.903	1.371
04	-2.694	-2.234	-2.163	1.311
05	1.32	-2.311	-1.92	-4.4
06	-2.234	-0.898	-3.903	1.243
07	0.046	-2.961	0.256	0.475
08	0.0	-3.126	0.957	-1.044
09	-0.879	0.275	0.687	-1.27
10	-0.26	0.425	-0.392	0.023

Standard thresholds

P-value	Threshold
0.001	4.62413
0.0005	5.58759
0.0001	7.43052