TLX2.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TLX2.H12RSNP.0.SM.B
Gene (human)	TLX2 (GeneCards)
Gene synonyms (human)	HOX11L1, NCX
Gene (mouse)	Tlx2
Gene synonyms (mouse)	Enx, Hox11l1, Ncx, Tlx1l1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	12
Consensus	nbYAATTARbbn
GC content	35.98%
Information content (bits; total / per base)	10.862 / 0.905
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8661

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.964	0.938	0.949	0.918	0.925	0.89
Overall, 2 experiments	best	0.964	0.94	0.949	0.918	0.927	0.892
Methyl HT-SELEX, 1 experiments	median	0.963	0.936	0.949	0.918	0.927	0.892
Methyl HT-SELEX, 1 experiments	best	0.963	0.936	0.949	0.918	0.927	0.892
Non-Methyl HT-SELEX, 1 experiments	median	0.964	0.94	0.948	0.918	0.924	0.889
Non-Methyl HT-SELEX, 1 experiments	best	0.964	0.94	0.948	0.918	0.924	0.889

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.624	0.088	0.486	0.222

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	NK-related {3.1.2} (TFClass)
TF subfamily	TLX {3.1.2.21} (TFClass)
TFClass ID	TFClass: 3.1.2.21.2
HGNC	HGNC:5057
MGI	MGI:1350935
EntrezGene (human)	GeneID:3196 (SSTAR profile)
EntrezGene (mouse)	GeneID:21909 (SSTAR profile)
UniProt ID (human)	TLX2_HUMAN
UniProt ID (mouse)	TLX2_MOUSE
UniProt AC (human)	O43763 (TFClass)
UniProt AC (mouse)	Q61663 (TFClass)
GRECO-DB-TF	yes

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

PCM	TLX2.H12RSNP.0.SM.B.pcm
PWM	TLX2.H12RSNP.0.SM.B.pwm
PFM	TLX2.H12RSNP.0.SM.B.pfm
Alignment	TLX2.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	TLX2.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	TLX2.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	TLX2.H12RSNP.0.SM.B_meme_format.meme
Transfac format	TLX2.H12RSNP.0.SM.B_transfac_format.txt
Homer format	TLX2.H12RSNP.0.SM.B_homer_format_0.001.txt TLX2.H12RSNP.0.SM.B_homer_format_0.0005.txt TLX2.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2139.0	2089.0	2449.0	1984.0
02	770.25	2512.25	2964.25	2414.25
03	304.0	2923.0	618.0	4816.0
04	6696.0	418.0	1528.0	19.0
05	8661.0	0.0	0.0	0.0
06	0.0	0.0	0.0	8661.0
07	0.0	0.0	0.0	8661.0
08	8661.0	0.0	0.0	0.0
09	1920.0	671.0	6054.0	16.0
10	655.0	3248.0	2671.0	2087.0
11	1047.0	1946.0	3093.0	2575.0
12	1958.0	2277.0	1929.0	2497.0

PFM

	A	C	G	T
01	0.247	0.241	0.283	0.229
02	0.089	0.29	0.342	0.279
03	0.035	0.337	0.071	0.556
04	0.773	0.048	0.176	0.002
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	1.0	0.0	0.0	0.0
09	0.222	0.077	0.699	0.002
10	0.076	0.375	0.308	0.241
11	0.121	0.225	0.357	0.297
12	0.226	0.263	0.223	0.288

PWM

	A	C	G	T
01	-0.012	-0.036	0.123	-0.087
02	-1.032	0.148	0.314	0.109
03	-1.957	0.3	-1.251	0.799
04	1.128	-1.64	-0.348	-4.624
05	1.386	-6.863	-6.863	-6.863
06	-6.863	-6.863	-6.863	1.386
07	-6.863	-6.863	-6.863	1.386
08	1.386	-6.863	-6.863	-6.863
09	-0.12	-1.169	1.028	-4.776
10	-1.193	0.405	0.21	-0.037
11	-0.725	-0.107	0.356	0.173
12	-0.101	0.05	-0.115	0.142

Standard thresholds

P-value	Threshold
0.001	4.56143
0.0005	5.897195
0.0001	7.727765