ALX1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ALX1.H12INVIVO.0.SM.D
Gene (human)	ALX1 (GeneCards)
Gene synonyms (human)	CART1
Gene (mouse)	Alx1
Gene synonyms (mouse)	Cart1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	20
Consensus	nvbTAATTRRRTTAvnnnnn
GC content	33.1%
Information content (bits; total / per base)	15.666 / 0.783
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7125

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.998	0.996	0.912	0.923	0.821	0.835
Overall, 4 experiments	best	1.0	0.999	0.996	0.994	0.984	0.98
Methyl HT-SELEX, 1 experiments	median	1.0	0.999	0.825	0.857	0.624	0.696
Methyl HT-SELEX, 1 experiments	best	1.0	0.999	0.825	0.857	0.624	0.696
Non-Methyl HT-SELEX, 3 experiments	median	0.997	0.995	0.993	0.99	0.966	0.96
Non-Methyl HT-SELEX, 3 experiments	best	0.998	0.997	0.996	0.994	0.984	0.98

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.776	0.441	0.72	0.45
batch 2	0.816	0.718	0.756	0.516

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	ALX {3.1.3.1} (TFClass)
TFClass ID	TFClass: 3.1.3.1.1
HGNC	HGNC:1494
MGI	MGI:104621
EntrezGene (human)	GeneID:8092 (SSTAR profile)
EntrezGene (mouse)	GeneID:216285 (SSTAR profile)
UniProt ID (human)	ALX1_HUMAN
UniProt ID (mouse)	ALX1_MOUSE
UniProt AC (human)	Q15699 (TFClass)
UniProt AC (mouse)	Q8C8B0 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	ALX1.H12INVIVO.0.SM.D.pcm
PWM	ALX1.H12INVIVO.0.SM.D.pwm
PFM	ALX1.H12INVIVO.0.SM.D.pfm
Alignment	ALX1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	ALX1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	ALX1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	ALX1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	ALX1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	ALX1.H12INVIVO.0.SM.D_homer_format_0.001.txt ALX1.H12INVIVO.0.SM.D_homer_format_0.0005.txt ALX1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1630.0	2253.0	2148.0	1094.0
02	1512.5	1762.5	2838.5	1011.5
03	495.0	3206.0	1623.0	1801.0
04	152.0	237.0	23.0	6713.0
05	6951.0	2.0	162.0	10.0
06	7125.0	0.0	0.0	0.0
07	2.0	80.0	3.0	7040.0
08	0.0	1149.0	90.0	5886.0
09	4453.0	407.0	1192.0	1073.0
10	3215.0	431.0	3468.0	11.0
11	5587.0	338.0	857.0	343.0
12	58.0	188.0	152.0	6727.0
13	288.0	506.0	125.0	6206.0
14	6316.0	136.0	351.0	322.0
15	2596.0	1338.0	2485.0	706.0
16	1045.0	2110.0	1453.0	2517.0
17	1174.0	1708.0	1879.0	2364.0
18	1574.0	2058.0	2096.0	1397.0
19	1534.5	2061.5	2119.5	1409.5
20	1451.0	2047.0	2090.0	1537.0

PFM

	A	C	G	T
01	0.229	0.316	0.301	0.154
02	0.212	0.247	0.398	0.142
03	0.069	0.45	0.228	0.253
04	0.021	0.033	0.003	0.942
05	0.976	0.0	0.023	0.001
06	1.0	0.0	0.0	0.0
07	0.0	0.011	0.0	0.988
08	0.0	0.161	0.013	0.826
09	0.625	0.057	0.167	0.151
10	0.451	0.06	0.487	0.002
11	0.784	0.047	0.12	0.048
12	0.008	0.026	0.021	0.944
13	0.04	0.071	0.018	0.871
14	0.886	0.019	0.049	0.045
15	0.364	0.188	0.349	0.099
16	0.147	0.296	0.204	0.353
17	0.165	0.24	0.264	0.332
18	0.221	0.289	0.294	0.196
19	0.215	0.289	0.297	0.198
20	0.204	0.287	0.293	0.216

PWM

	A	C	G	T
01	-0.089	0.235	0.187	-0.487
02	-0.163	-0.011	0.465	-0.565
03	-1.277	0.587	-0.093	0.011
04	-2.448	-2.009	-4.259	1.326
05	1.361	-6.047	-2.385	-4.983
06	1.385	-6.69	-6.69	-6.69
07	-6.047	-3.077	-5.834	1.373
08	-6.69	-0.438	-2.962	1.194
09	0.916	-1.472	-0.401	-0.506
10	0.59	-1.415	0.666	-4.905
11	1.142	-1.657	-0.73	-1.642
12	-3.388	-2.238	-2.448	1.328
13	-1.816	-1.255	-2.64	1.247
14	1.265	-2.557	-1.619	-1.705
15	0.376	-0.286	0.333	-0.924
16	-0.532	0.169	-0.203	0.345
17	-0.416	-0.042	0.053	0.283
18	-0.124	0.144	0.163	-0.243
19	-0.149	0.146	0.174	-0.234
20	-0.205	0.139	0.16	-0.147

Standard thresholds

P-value	Threshold
0.001	2.09491
0.0005	3.46966
0.0001	6.26466