HXA13.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA13.H12INVITRO.1.SM.B
Gene (human)	HOXA13 (GeneCards)
Gene synonyms (human)	HOX1J
Gene (mouse)	Hoxa13
Gene synonyms (mouse)	Hox-1.10
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	12
Consensus	ndTTTACGAGvn
GC content	40.07%
Information content (bits; total / per base)	13.598 / 1.133
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8693

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	4 (27)	0.858	0.92	0.77	0.859	0.779	0.863	2.743	3.818	83.745	215.409

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.998	0.996	0.992	0.989	0.937	0.926
Overall, 5 experiments	best	0.999	0.999	0.998	0.997	0.973	0.97
Methyl HT-SELEX, 2 experiments	median	0.999	0.998	0.995	0.993	0.944	0.943
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.998	0.997	0.972	0.969
Non-Methyl HT-SELEX, 3 experiments	median	0.996	0.993	0.984	0.978	0.937	0.926
Non-Methyl HT-SELEX, 3 experiments	best	0.999	0.999	0.998	0.997	0.973	0.97

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: 3.1.1.8.14
HGNC	HGNC:5102
MGI	MGI:96173
EntrezGene (human)	GeneID:3209 (SSTAR profile)
EntrezGene (mouse)	GeneID:15398 (SSTAR profile)
UniProt ID (human)	HXA13_HUMAN
UniProt ID (mouse)	HXA13_MOUSE
UniProt AC (human)	P31271 (TFClass)
UniProt AC (mouse)	Q62424 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 4 mouse
HT-SELEX	3
Methyl-HT-SELEX	2

PCM	HXA13.H12INVITRO.1.SM.B.pcm
PWM	HXA13.H12INVITRO.1.SM.B.pwm
PFM	HXA13.H12INVITRO.1.SM.B.pfm
Alignment	HXA13.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	HXA13.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	HXA13.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	HXA13.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	HXA13.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	HXA13.H12INVITRO.1.SM.B_homer_format_0.001.txt HXA13.H12INVITRO.1.SM.B_homer_format_0.0005.txt HXA13.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2209.5	1674.5	2791.5	2017.5
02	1633.75	861.75	1872.75	4324.75
03	277.0	46.0	280.0	8090.0
04	113.0	11.0	15.0	8554.0
05	864.0	21.0	8.0	7800.0
06	8689.0	0.0	0.0	4.0
07	0.0	7522.0	0.0	1171.0
08	84.0	2.0	8559.0	48.0
09	8495.0	36.0	118.0	44.0
10	52.0	695.0	7338.0	608.0
11	1581.5	3234.5	2661.5	1215.5
12	1772.75	1895.75	2154.75	2869.75

PFM

	A	C	G	T
01	0.254	0.193	0.321	0.232
02	0.188	0.099	0.215	0.497
03	0.032	0.005	0.032	0.931
04	0.013	0.001	0.002	0.984
05	0.099	0.002	0.001	0.897
06	1.0	0.0	0.0	0.0
07	0.0	0.865	0.0	0.135
08	0.01	0.0	0.985	0.006
09	0.977	0.004	0.014	0.005
10	0.006	0.08	0.844	0.07
11	0.182	0.372	0.306	0.14
12	0.204	0.218	0.248	0.33

PWM

	A	C	G	T
01	0.017	-0.26	0.25	-0.074
02	-0.285	-0.923	-0.149	0.688
03	-2.053	-3.808	-2.042	1.314
04	-2.938	-5.1	-4.836	1.369
05	-0.921	-4.538	-5.356	1.277
06	1.385	-6.866	-6.866	-5.85
07	-6.866	1.241	-6.866	-0.617
08	-3.228	-6.234	1.37	-3.768
09	1.362	-4.04	-2.895	-3.851
10	-3.691	-1.138	1.216	-1.271
11	-0.317	0.397	0.202	-0.58
12	-0.203	-0.136	-0.009	0.278

Standard thresholds

P-value	Threshold
0.001	2.76068
0.0005	4.114185
0.0001	6.906205