LHX6.H12INVITRO.2.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX6.H12INVITRO.2.M.C
Gene (human)	LHX6 (GeneCards)
Gene synonyms (human)	LHX6.1
Gene (mouse)	Lhx6
Gene synonyms (mouse)	Lhx6.1
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	13
Consensus	nvvYTAACKAGbn
GC content	46.08%
Information content (bits; total / per base)	12.655 / 0.973
Data sources	Methyl-HT-SELEX
Aligned words	6243

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
Mouse	2 (12)	0.69	0.802	0.494	0.662	0.584	0.753	1.332	2.035	26.779	51.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.792	0.769	0.759	0.743	0.733	0.72
Overall, 4 experiments	best	0.992	0.987	0.985	0.976	0.971	0.958
Methyl HT-SELEX, 1 experiments	median	0.992	0.987	0.985	0.976	0.971	0.958
Methyl HT-SELEX, 1 experiments	best	0.992	0.987	0.985	0.976	0.971	0.958
Non-Methyl HT-SELEX, 3 experiments	median	0.611	0.583	0.555	0.548	0.527	0.529
Non-Methyl HT-SELEX, 3 experiments	best	0.973	0.954	0.962	0.938	0.939	0.911

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.687	0.217	0.584	0.284

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HD-LIM {3.1.5} (TFClass)
TF subfamily	LHX6-like {3.1.5.5} (TFClass)
TFClass ID	TFClass: 3.1.5.5.1
HGNC	HGNC:21735
MGI	MGI:1306803
EntrezGene (human)	GeneID:26468 (SSTAR profile)
EntrezGene (mouse)	GeneID:16874 (SSTAR profile)
UniProt ID (human)	LHX6_HUMAN
UniProt ID (mouse)	LHX6_MOUSE
UniProt AC (human)	Q9UPM6 (TFClass)
UniProt AC (mouse)	Q9R1R0 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	LHX6.H12INVITRO.2.M.C.pcm
PWM	LHX6.H12INVITRO.2.M.C.pwm
PFM	LHX6.H12INVITRO.2.M.C.pfm
Alignment	LHX6.H12INVITRO.2.M.C.words.tsv
Threshold to P-value map	LHX6.H12INVITRO.2.M.C.thr
Motif in other formats
JASPAR format	LHX6.H12INVITRO.2.M.C_jaspar_format.txt
MEME format	LHX6.H12INVITRO.2.M.C_meme_format.meme
Transfac format	LHX6.H12INVITRO.2.M.C_transfac_format.txt
Homer format	LHX6.H12INVITRO.2.M.C_homer_format_0.001.txt LHX6.H12INVITRO.2.M.C_homer_format_0.0005.txt LHX6.H12INVITRO.2.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1549.75	1492.75	1526.75	1673.75
02	1159.5	2955.5	1439.5	688.5
03	1904.0	1337.0	2904.0	98.0
04	76.0	3505.0	199.0	2463.0
05	0.0	0.0	0.0	6243.0
06	6241.0	0.0	2.0	0.0
07	6243.0	0.0	0.0	0.0
08	0.0	3910.0	0.0	2333.0
09	0.0	202.0	4089.0	1952.0
10	6222.0	0.0	21.0	0.0
11	32.0	999.0	4955.0	257.0
12	503.5	2766.5	2153.5	819.5
13	1432.0	1607.0	1335.0	1869.0

PFM

	A	C	G	T
01	0.248	0.239	0.245	0.268
02	0.186	0.473	0.231	0.11
03	0.305	0.214	0.465	0.016
04	0.012	0.561	0.032	0.395
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.626	0.0	0.374
09	0.0	0.032	0.655	0.313
10	0.997	0.0	0.003	0.0
11	0.005	0.16	0.794	0.041
12	0.081	0.443	0.345	0.131
13	0.229	0.257	0.214	0.299

PWM

	A	C	G	T
01	-0.007	-0.044	-0.022	0.07
02	-0.297	0.638	-0.081	-0.817
03	0.199	-0.155	0.62	-2.747
04	-2.995	0.808	-2.05	0.456
05	-6.573	-6.573	-6.573	1.385
06	1.385	-6.573	-5.923	-6.573
07	1.385	-6.573	-6.573	-6.573
08	-6.573	0.918	-6.573	0.402
09	-6.573	-2.035	0.962	0.223
10	1.382	-6.573	-4.211	-6.573
11	-3.823	-0.445	1.154	-1.797
12	-1.128	0.572	0.322	-0.643
13	-0.086	0.029	-0.156	0.18

Standard thresholds

P-value	Threshold
0.001	2.29447
0.0005	4.31421
0.0001	7.57248