ISX.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ISX.H12INVIVO.0.SM.D
Gene (human)	ISX (GeneCards)
Gene synonyms (human)	RAXLX
Gene (mouse)	Isx
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nvbTAATTGRnn
GC content	34.0%
Information content (bits; total / per base)	12.194 / 1.016
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7723

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.988	0.978	0.984	0.972	0.974	0.959
Overall, 8 experiments	best	0.995	0.992	0.994	0.99	0.991	0.985
Methyl HT-SELEX, 2 experiments	median	0.991	0.983	0.987	0.978	0.979	0.968
Methyl HT-SELEX, 2 experiments	best	0.995	0.991	0.994	0.989	0.99	0.984
Non-Methyl HT-SELEX, 6 experiments	median	0.987	0.976	0.977	0.963	0.902	0.901
Non-Methyl HT-SELEX, 6 experiments	best	0.995	0.992	0.994	0.99	0.991	0.985

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.964	0.75	0.932	0.549
batch 2	0.742	0.333	0.748	0.561

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	Paired-related HD {3.1.3} (TFClass)
TF subfamily	ISX {3.1.3.12} (TFClass)
TFClass ID	TFClass: 3.1.3.12.1
HGNC	HGNC:28084
MGI	MGI:1918847
EntrezGene (human)	GeneID:91464 (SSTAR profile)
EntrezGene (mouse)	GeneID:71597 (SSTAR profile)
UniProt ID (human)	ISX_HUMAN
UniProt ID (mouse)	ISX_MOUSE
UniProt AC (human)	Q2M1V0 (TFClass)
UniProt AC (mouse)	A1A546 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	ISX.H12INVIVO.0.SM.D.pcm
PWM	ISX.H12INVIVO.0.SM.D.pwm
PFM	ISX.H12INVIVO.0.SM.D.pfm
Alignment	ISX.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	ISX.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	ISX.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	ISX.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	ISX.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	ISX.H12INVIVO.0.SM.D_homer_format_0.001.txt ISX.H12INVIVO.0.SM.D_homer_format_0.0005.txt ISX.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1944.0	1799.0	2353.0	1627.0
02	1707.0	1316.0	3623.0	1077.0
03	245.0	2801.0	1979.0	2698.0
04	0.0	2.0	0.0	7721.0
05	7723.0	0.0	0.0	0.0
06	7723.0	0.0	0.0	0.0
07	0.0	0.0	0.0	7723.0
08	0.0	0.0	0.0	7723.0
09	2816.0	0.0	4907.0	0.0
10	1403.0	861.0	5030.0	429.0
11	1498.0	1643.0	1939.0	2643.0
12	1410.25	1616.25	1637.25	3059.25

PFM

	A	C	G	T
01	0.252	0.233	0.305	0.211
02	0.221	0.17	0.469	0.139
03	0.032	0.363	0.256	0.349
04	0.0	0.0	0.0	1.0
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.365	0.0	0.635	0.0
10	0.182	0.111	0.651	0.056
11	0.194	0.213	0.251	0.342
12	0.183	0.209	0.212	0.396

PWM

	A	C	G	T
01	0.007	-0.071	0.198	-0.171
02	-0.123	-0.383	0.629	-0.583
03	-2.056	0.372	0.025	0.334
04	-6.761	-6.123	-6.761	1.385
05	1.385	-6.761	-6.761	-6.761
06	1.385	-6.761	-6.761	-6.761
07	-6.761	-6.761	-6.761	1.385
08	-6.761	-6.761	-6.761	1.385
09	0.377	-6.761	0.932	-6.761
10	-0.319	-0.806	0.957	-1.5
11	-0.253	-0.161	0.004	0.314
12	-0.314	-0.178	-0.165	0.46

Standard thresholds

P-value	Threshold
0.001	0.824115
0.0005	2.334675
0.0001	7.926275