LHX9.H12RSNP.1.M.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LHX9.H12RSNP.1.M.B
Gene (human)	LHX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lhx9
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	14
Consensus	nbvRTTAACGAGbn
GC content	36.66%
Information content (bits; total / per base)	14.379 / 1.027
Data sources	Methyl-HT-SELEX
Aligned words	334

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
Human	1 (5)	0.779	0.807	0.634	0.672	0.672	0.681	1.77	1.786	58.187	84.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.927	0.89	0.85	0.822	0.743	0.738
Overall, 8 experiments	best	0.97	0.949	0.957	0.931	0.922	0.894
Methyl HT-SELEX, 3 experiments	median	0.964	0.94	0.943	0.913	0.871	0.847
Methyl HT-SELEX, 3 experiments	best	0.97	0.949	0.957	0.931	0.922	0.894
Non-Methyl HT-SELEX, 5 experiments	median	0.904	0.863	0.774	0.755	0.639	0.656
Non-Methyl HT-SELEX, 5 experiments	best	0.962	0.935	0.94	0.908	0.88	0.85

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.805	0.277	0.782	0.463
batch 2	0.664	0.407	0.557	0.44

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	LHX2-like {3.1.5.3} (TFClass)
TFClass ID	TFClass: 3.1.5.3.2
HGNC	HGNC:14222
MGI	MGI:1316721
EntrezGene (human)	GeneID:56956 (SSTAR profile)
EntrezGene (mouse)	GeneID:16876 (SSTAR profile)
UniProt ID (human)	LHX9_HUMAN
UniProt ID (mouse)	LHX9_MOUSE
UniProt AC (human)	Q9NQ69 (TFClass)
UniProt AC (mouse)	Q9WUH2 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	5
Methyl-HT-SELEX	3

PCM	LHX9.H12RSNP.1.M.B.pcm
PWM	LHX9.H12RSNP.1.M.B.pwm
PFM	LHX9.H12RSNP.1.M.B.pfm
Alignment	LHX9.H12RSNP.1.M.B.words.tsv
Threshold to P-value map	LHX9.H12RSNP.1.M.B.thr
Motif in other formats
JASPAR format	LHX9.H12RSNP.1.M.B_jaspar_format.txt
MEME format	LHX9.H12RSNP.1.M.B_meme_format.meme
Transfac format	LHX9.H12RSNP.1.M.B_transfac_format.txt
Homer format	LHX9.H12RSNP.1.M.B_homer_format_0.001.txt LHX9.H12RSNP.1.M.B_homer_format_0.0005.txt LHX9.H12RSNP.1.M.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	104.75	73.75	74.75	80.75
02	32.25	69.25	59.25	173.25
03	136.0	137.0	39.0	22.0
04	184.0	12.0	137.0	1.0
05	1.0	44.0	1.0	288.0
06	0.0	0.0	0.0	334.0
07	334.0	0.0	0.0	0.0
08	334.0	0.0	0.0	0.0
09	0.0	183.0	0.0	151.0
10	0.0	0.0	190.0	144.0
11	332.0	0.0	2.0	0.0
12	7.0	14.0	295.0	18.0
13	36.75	172.75	77.75	46.75
14	116.25	70.25	62.25	85.25

PFM

	A	C	G	T
01	0.314	0.221	0.224	0.242
02	0.097	0.207	0.177	0.519
03	0.407	0.41	0.117	0.066
04	0.551	0.036	0.41	0.003
05	0.003	0.132	0.003	0.862
06	0.0	0.0	0.0	1.0
07	1.0	0.0	0.0	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.548	0.0	0.452
10	0.0	0.0	0.569	0.431
11	0.994	0.0	0.006	0.0
12	0.021	0.042	0.883	0.054
13	0.11	0.517	0.233	0.14
14	0.348	0.21	0.186	0.255

PWM

	A	C	G	T
01	0.223	-0.122	-0.109	-0.033
02	-0.925	-0.184	-0.336	0.721
03	0.481	0.488	-0.742	-1.287
04	0.781	-1.843	0.488	-3.545
05	-3.545	-0.625	-3.545	1.226
06	-4.069	-4.069	-4.069	1.373
07	1.373	-4.069	-4.069	-4.069
08	1.373	-4.069	-4.069	-4.069
09	-4.069	0.775	-4.069	0.585
10	-4.069	-4.069	0.813	0.538
11	1.367	-4.069	-3.203	-4.069
12	-2.308	-1.704	1.25	-1.474
13	-0.799	0.718	-0.07	-0.567
14	0.326	-0.17	-0.288	0.02

Standard thresholds

P-value	Threshold
0.001	2.91971
0.0005	4.24961
0.0001	6.79081