HXB4.H14INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB4.H14INVIVO.1.PSM.A
Gene (human)	HOXB4 (GeneCards)
Gene synonyms (human)	HOX2F
Gene (mouse)	Hoxb4
Gene synonyms (mouse)	Hox-2.6, Hoxb-4
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	9
Consensus	RYWRATKRS
GC content	36.77%
Information content (bits; total / per base)	9.019 / 1.002
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000
Previous names	HXB4.H12INVIVO.1.PSM.A

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
Mouse	3 (21)	0.826	0.859	0.693	0.751	0.796	0.818	2.325	2.559	282.854	365.377

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.872	0.819	0.801	0.759	0.717	0.695
Overall, 2 experiments	best	0.911	0.861	0.873	0.821	0.806	0.763
Methyl HT-SELEX, 1 experiments	median	0.833	0.778	0.73	0.696	0.628	0.626
Methyl HT-SELEX, 1 experiments	best	0.833	0.778	0.73	0.696	0.628	0.626
Non-Methyl HT-SELEX, 1 experiments	median	0.911	0.861	0.873	0.821	0.806	0.763
Non-Methyl HT-SELEX, 1 experiments	best	0.911	0.861	0.873	0.821	0.806	0.763

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	HOX4 {3.1.1.4} (TFClass)
TFClass ID	TFClass: 3.1.1.4.2
HGNC	HGNC:5115
MGI	MGI:96185
EntrezGene (human)	GeneID:3214 (SSTAR profile)
EntrezGene (mouse)	GeneID:15412 (SSTAR profile)
UniProt ID (human)	HXB4_HUMAN
UniProt ID (mouse)	HXB4_MOUSE
UniProt AC (human)	P17483 (TFClass)
UniProt AC (mouse)	P10284 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXB4.H14INVIVO.1.PSM.A.pcm
PWM	HXB4.H14INVIVO.1.PSM.A.pwm
PFM	HXB4.H14INVIVO.1.PSM.A.pfm
Threshold to P-value map	HXB4.H14INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	HXB4.H14INVIVO.1.PSM.A_jaspar_format.txt
MEME format	HXB4.H14INVIVO.1.PSM.A_meme_format.meme
Transfac format	HXB4.H14INVIVO.1.PSM.A_transfac_format.txt
Homer format	HXB4.H14INVIVO.1.PSM.A_homer_format_0.001.txt HXB4.H14INVIVO.1.PSM.A_homer_format_0.0005.txt HXB4.H14INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	648.0	134.0	163.0	55.0
02	28.0	327.0	64.0	581.0
03	146.0	11.0	117.0	726.0
04	682.0	7.0	295.0	16.0
05	1000.0	0.0	0.0	0.0
06	0.0	25.0	0.0	975.0
07	41.0	69.0	664.0	226.0
08	462.0	6.0	474.0	58.0
09	15.0	691.0	262.0	32.0

PFM

	A	C	G	T
01	0.648	0.134	0.163	0.055
02	0.028	0.327	0.064	0.581
03	0.146	0.011	0.117	0.726
04	0.682	0.007	0.295	0.016
05	1.0	0.0	0.0	0.0
06	0.0	0.025	0.0	0.975
07	0.041	0.069	0.664	0.226
08	0.462	0.006	0.474	0.058
09	0.015	0.691	0.262	0.032

PWM

	A	C	G	T
01	0.948	-0.618	-0.424	-1.49
02	-2.136	0.267	-1.343	0.839
03	-0.533	-2.985	-0.752	1.062
04	0.999	-3.362	0.164	-2.653
05	1.381	-4.982	-4.982	-4.982
06	-4.982	-2.243	-4.982	1.356
07	-1.774	-1.27	0.973	-0.1
08	0.611	-3.484	0.636	-1.439
09	-2.711	1.012	0.047	-2.01

Standard thresholds

P-value	Threshold
0.001	5.103385
0.0005	5.914615
0.0001	7.29157