HXC9.H12INVIVO.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC9.H12INVIVO.1.S.C
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	1
Quality	C

Motif length	12
Consensus	ndTTTATGRYbn
GC content	34.96%
Information content (bits; total / per base)	10.816 / 0.901
Data sources	HT-SELEX
Aligned words	9246

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)	0.772	0.808	0.627	0.669	0.802	0.818	2.327	2.436	54.337	75.921
Mouse	3 (19)	0.781	0.809	0.632	0.657	0.765	0.812	2.154	2.381	82.222	89.337

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.985	0.975	0.976	0.962	0.948	0.93
Overall, 2 experiments	best	0.989	0.981	0.982	0.971	0.951	0.936
Methyl HT-SELEX, 1 experiments	median	0.989	0.981	0.982	0.971	0.951	0.936
Methyl HT-SELEX, 1 experiments	best	0.989	0.981	0.982	0.971	0.951	0.936
Non-Methyl HT-SELEX, 1 experiments	median	0.981	0.968	0.971	0.953	0.945	0.923
Non-Methyl HT-SELEX, 1 experiments	best	0.981	0.968	0.971	0.953	0.945	0.923

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.H12INVIVO.1.S.C.pcm
PWM	HXC9.H12INVIVO.1.S.C.pwm
PFM	HXC9.H12INVIVO.1.S.C.pfm
Alignment	HXC9.H12INVIVO.1.S.C.words.tsv
Threshold to P-value map	HXC9.H12INVIVO.1.S.C.thr
Motif in other formats
JASPAR format	HXC9.H12INVIVO.1.S.C_jaspar_format.txt
MEME format	HXC9.H12INVIVO.1.S.C_meme_format.meme
Transfac format	HXC9.H12INVIVO.1.S.C_transfac_format.txt
Homer format	HXC9.H12INVIVO.1.S.C_homer_format_0.001.txt HXC9.H12INVIVO.1.S.C_homer_format_0.0005.txt HXC9.H12INVIVO.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2768.75	2051.75	2390.75	2034.75
02	1891.5	1149.5	1418.5	4786.5
03	399.0	31.0	224.0	8592.0
04	20.0	3.0	2.0	9221.0
05	3171.0	0.0	2.0	6073.0
06	9246.0	0.0	0.0	0.0
07	3.0	3420.0	3.0	5820.0
08	19.0	36.0	7910.0	1281.0
09	6064.0	43.0	2858.0	281.0
10	175.0	5577.0	1713.0	1781.0
11	1295.5	3787.5	1870.5	2292.5
12	1990.5	2206.5	2092.5	2956.5

PFM

	A	C	G	T
01	0.299	0.222	0.259	0.22
02	0.205	0.124	0.153	0.518
03	0.043	0.003	0.024	0.929
04	0.002	0.0	0.0	0.997
05	0.343	0.0	0.0	0.657
06	1.0	0.0	0.0	0.0
07	0.0	0.37	0.0	0.629
08	0.002	0.004	0.856	0.139
09	0.656	0.005	0.309	0.03
10	0.019	0.603	0.185	0.193
11	0.14	0.41	0.202	0.248
12	0.215	0.239	0.226	0.32

PWM

	A	C	G	T
01	0.18	-0.119	0.034	-0.127
02	-0.2	-0.698	-0.488	0.727
03	-1.752	-4.242	-2.325	1.312
04	-4.643	-6.082	-6.292	1.383
05	0.316	-6.921	-6.292	0.965
06	1.386	-6.921	-6.921	-6.921
07	-6.082	0.391	-6.082	0.923
08	-4.689	-4.102	1.23	-0.589
09	0.964	-3.934	0.212	-2.1
10	-2.569	0.88	-0.299	-0.26
11	-0.578	0.493	-0.211	-0.008
12	-0.149	-0.046	-0.099	0.246

Standard thresholds

P-value	Threshold
0.001	4.426265
0.0005	5.70517
0.0001	7.712655