HXC9.H12RSNP.2.M.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC9.H12RSNP.2.M.D
Gene (human)	HOXC9 (GeneCards)
Gene synonyms (human)	HOX3B
Gene (mouse)	Hoxc9
Gene synonyms (mouse)	Hox-3.2, Hoxc-9
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	D

Motif length	13
Consensus	nhTTTACGAYbnn
GC content	39.46%
Information content (bits; total / per base)	12.953 / 0.996
Data sources	Methyl-HT-SELEX
Aligned words	7484

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	1 (7)	0.736	0.771	0.555	0.602	0.75	0.767	2.005	2.083	33.149	43.886
Mouse	3 (19)	0.75	0.781	0.578	0.611	0.718	0.767	1.904	2.11	55.444	73.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.989	0.983	0.969	0.958	0.926	0.907
Overall, 2 experiments	best	0.994	0.991	0.98	0.973	0.937	0.923
Methyl HT-SELEX, 1 experiments	median	0.994	0.991	0.98	0.973	0.937	0.923
Methyl HT-SELEX, 1 experiments	best	0.994	0.991	0.98	0.973	0.937	0.923
Non-Methyl HT-SELEX, 1 experiments	median	0.985	0.975	0.958	0.942	0.915	0.891
Non-Methyl HT-SELEX, 1 experiments	best	0.985	0.975	0.958	0.942	0.915	0.891

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: 3.1.1.8.3
HGNC	HGNC:5130
MGI	MGI:96199
EntrezGene (human)	GeneID:3225 (SSTAR profile)
EntrezGene (mouse)	GeneID:15427 (SSTAR profile)
UniProt ID (human)	HXC9_HUMAN
UniProt ID (mouse)	HXC9_MOUSE
UniProt AC (human)	P31274 (TFClass)
UniProt AC (mouse)	P09633 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 3 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	HXC9.H12RSNP.2.M.D.pcm
PWM	HXC9.H12RSNP.2.M.D.pwm
PFM	HXC9.H12RSNP.2.M.D.pfm
Alignment	HXC9.H12RSNP.2.M.D.words.tsv
Threshold to P-value map	HXC9.H12RSNP.2.M.D.thr
Motif in other formats
JASPAR format	HXC9.H12RSNP.2.M.D_jaspar_format.txt
MEME format	HXC9.H12RSNP.2.M.D_meme_format.meme
Transfac format	HXC9.H12RSNP.2.M.D_transfac_format.txt
Homer format	HXC9.H12RSNP.2.M.D_homer_format_0.001.txt HXC9.H12RSNP.2.M.D_homer_format_0.0005.txt HXC9.H12RSNP.2.M.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2103.75	1969.75	1810.75	1599.75
02	1406.75	1224.75	1154.75	3697.75
03	325.0	21.0	135.0	7003.0
04	12.0	4.0	2.0	7466.0
05	1885.0	0.0	1.0	5598.0
06	7484.0	0.0	0.0	0.0
07	0.0	5864.0	0.0	1620.0
08	0.0	0.0	7428.0	56.0
09	7120.0	2.0	330.0	32.0
10	8.0	5397.0	687.0	1392.0
11	996.0	3423.0	1865.0	1200.0
12	1442.75	1913.75	1391.75	2735.75
13	1762.25	2208.25	1561.25	1952.25

PFM

	A	C	G	T
01	0.281	0.263	0.242	0.214
02	0.188	0.164	0.154	0.494
03	0.043	0.003	0.018	0.936
04	0.002	0.001	0.0	0.998
05	0.252	0.0	0.0	0.748
06	1.0	0.0	0.0	0.0
07	0.0	0.784	0.0	0.216
08	0.0	0.0	0.993	0.007
09	0.951	0.0	0.044	0.004
10	0.001	0.721	0.092	0.186
11	0.133	0.457	0.249	0.16
12	0.193	0.256	0.186	0.366
13	0.235	0.295	0.209	0.261

PWM

	A	C	G	T
01	0.117	0.051	-0.033	-0.156
02	-0.285	-0.423	-0.482	0.681
03	-1.745	-4.39	-2.614	1.319
04	-4.88	-5.706	-6.093	1.383
05	0.007	-6.733	-6.363	1.095
06	1.385	-6.733	-6.733	-6.733
07	-6.733	1.142	-6.733	-0.144
08	-6.733	-6.733	1.378	-3.471
09	1.336	-6.093	-1.73	-4.002
10	-5.21	1.059	-1.0	-0.295
11	-0.629	0.604	-0.003	-0.443
12	-0.26	0.023	-0.296	0.38
13	-0.06	0.166	-0.181	0.042

Standard thresholds

P-value	Threshold
0.001	2.65736
0.0005	4.20986
0.0001	7.424185