TLX3.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TLX3.H12INVITRO.0.SM.B
Gene (human)	TLX3 (GeneCards)
Gene synonyms (human)	HOX11L2
Gene (mouse)	Tlx3
Gene synonyms (mouse)	Hox11l2, Rnx, Tlx1l2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	12
Consensus	nhSTTAAYKRnn
GC content	35.32%
Information content (bits; total / per base)	9.872 / 0.823
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2244

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.724	0.669	0.662	0.62	0.607	0.585
Overall, 3 experiments	best	0.785	0.724	0.72	0.671	0.652	0.625
Methyl HT-SELEX, 2 experiments	median	0.755	0.697	0.687	0.645	0.624	0.603
Methyl HT-SELEX, 2 experiments	best	0.785	0.724	0.72	0.671	0.652	0.625
Non-Methyl HT-SELEX, 1 experiments	median	0.717	0.659	0.662	0.619	0.607	0.585
Non-Methyl HT-SELEX, 1 experiments	best	0.717	0.659	0.662	0.619	0.607	0.585

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.592	0.127	0.514	0.302

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: 3.1.2.21.3
HGNC	HGNC:13532
MGI	MGI:1351209
EntrezGene (human)	GeneID:30012 (SSTAR profile)
EntrezGene (mouse)	GeneID:27140 (SSTAR profile)
UniProt ID (human)	TLX3_HUMAN
UniProt ID (mouse)	TLX3_MOUSE
UniProt AC (human)	O43711 (TFClass)
UniProt AC (mouse)	O55144 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	2

PCM	TLX3.H12INVITRO.0.SM.B.pcm
PWM	TLX3.H12INVITRO.0.SM.B.pwm
PFM	TLX3.H12INVITRO.0.SM.B.pfm
Alignment	TLX3.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	TLX3.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	TLX3.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	TLX3.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	TLX3.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	TLX3.H12INVITRO.0.SM.B_homer_format_0.001.txt TLX3.H12INVITRO.0.SM.B_homer_format_0.0005.txt TLX3.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	762.25	351.25	504.25	626.25
02	417.75	1152.75	291.75	381.75
03	421.0	450.0	1278.0	95.0
04	22.0	176.0	41.0	2005.0
05	0.0	12.0	0.0	2232.0
06	2243.0	0.0	1.0	0.0
07	2244.0	0.0	0.0	0.0
08	195.0	391.0	195.0	1463.0
09	144.0	195.0	743.0	1162.0
10	1025.0	36.0	1146.0	37.0
11	549.75	635.75	696.75	361.75
12	444.0	624.0	591.0	585.0

PFM

	A	C	G	T
01	0.34	0.157	0.225	0.279
02	0.186	0.514	0.13	0.17
03	0.188	0.201	0.57	0.042
04	0.01	0.078	0.018	0.893
05	0.0	0.005	0.0	0.995
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.087	0.174	0.087	0.652
09	0.064	0.087	0.331	0.518
10	0.457	0.016	0.511	0.016
11	0.245	0.283	0.31	0.161
12	0.198	0.278	0.263	0.261

PWM

	A	C	G	T
01	0.306	-0.466	-0.106	0.11
02	-0.294	0.718	-0.651	-0.383
03	-0.286	-0.22	0.821	-1.759
04	-3.158	-1.152	-2.574	1.271
05	-5.676	-3.699	-5.676	1.378
06	1.383	-5.676	-5.258	-5.676
07	1.384	-5.676	-5.676	-5.676
08	-1.05	-0.36	-1.05	0.956
09	-1.35	-1.05	0.28	0.726
10	0.601	-2.697	0.713	-2.671
11	-0.02	0.125	0.216	-0.437
12	-0.233	0.106	0.052	0.042

Standard thresholds

P-value	Threshold
0.001	5.02587
0.0005	5.94969
0.0001	7.50333