LHX6.H12CORE.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX6.H12CORE.1.S.B
Gene (human)	LHX6 (GeneCards)
Gene synonyms (human)	LHX6.1
Gene (mouse)	Lhx6
Gene synonyms (mouse)	Lhx6.1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	14
Consensus	nnvSTAATTARbbn
GC content	40.71%
Information content (bits; total / per base)	12.657 / 0.904
Data sources	HT-SELEX
Aligned words	8423

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)	0.841	0.889	0.7	0.754	0.75	0.834	1.99	2.449	118.876	158.174

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.818	0.805	0.775	0.77	0.75	0.746
Overall, 4 experiments	best	0.991	0.984	0.986	0.976	0.978	0.966
Methyl HT-SELEX, 1 experiments	median	0.989	0.982	0.982	0.971	0.966	0.951
Methyl HT-SELEX, 1 experiments	best	0.989	0.982	0.982	0.971	0.966	0.951
Non-Methyl HT-SELEX, 3 experiments	median	0.646	0.627	0.568	0.569	0.534	0.541
Non-Methyl HT-SELEX, 3 experiments	best	0.991	0.984	0.986	0.976	0.978	0.966

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.95	0.827	0.922	0.606

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.H12CORE.1.S.B.pcm
PWM	LHX6.H12CORE.1.S.B.pwm
PFM	LHX6.H12CORE.1.S.B.pfm
Alignment	LHX6.H12CORE.1.S.B.words.tsv
Threshold to P-value map	LHX6.H12CORE.1.S.B.thr
Motif in other formats
JASPAR format	LHX6.H12CORE.1.S.B_jaspar_format.txt
MEME format	LHX6.H12CORE.1.S.B_meme_format.meme
Transfac format	LHX6.H12CORE.1.S.B_transfac_format.txt
Homer format	LHX6.H12CORE.1.S.B_homer_format_0.001.txt LHX6.H12CORE.1.S.B_homer_format_0.0005.txt LHX6.H12CORE.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2406.25	1813.25	2194.25	2009.25
02	2142.75	1719.75	2872.75	1687.75
03	1265.0	3129.0	2962.0	1067.0
04	14.0	3907.0	4245.0	257.0
05	0.0	1498.0	0.0	6925.0
06	8421.0	2.0	0.0	0.0
07	8423.0	0.0	0.0	0.0
08	0.0	0.0	0.0	8423.0
09	0.0	2639.0	0.0	5784.0
10	8423.0	0.0	0.0	0.0
11	2379.0	647.0	5256.0	141.0
12	64.0	3692.0	1952.0	2715.0
13	1225.5	1863.5	3644.5	1689.5
14	2323.0	2184.0	1784.0	2132.0

PFM

	A	C	G	T
01	0.286	0.215	0.261	0.239
02	0.254	0.204	0.341	0.2
03	0.15	0.371	0.352	0.127
04	0.002	0.464	0.504	0.031
05	0.0	0.178	0.0	0.822
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.313	0.0	0.687
10	1.0	0.0	0.0	0.0
11	0.282	0.077	0.624	0.017
12	0.008	0.438	0.232	0.322
13	0.145	0.221	0.433	0.201
14	0.276	0.259	0.212	0.253

PWM

	A	C	G	T
01	0.133	-0.149	0.041	-0.047
02	0.017	-0.202	0.31	-0.221
03	-0.509	0.396	0.341	-0.679
04	-4.865	0.618	0.701	-2.096
05	-6.838	-0.34	-6.838	1.19
06	1.385	-6.204	-6.838	-6.838
07	1.385	-6.838	-6.838	-6.838
08	-6.838	-6.838	-6.838	1.385
09	-6.838	0.226	-6.838	1.01
10	1.385	-6.838	-6.838	-6.838
11	0.122	-1.178	0.914	-2.689
12	-3.46	0.561	-0.076	0.254
13	-0.541	-0.122	0.548	-0.22
14	0.098	0.036	-0.166	0.012

Standard thresholds

P-value	Threshold
0.001	1.29291
0.0005	3.634815
0.0001	7.752765