TGIF2.H14RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TGIF2.H14RSNP.1.PSM.A
Gene (human)	TGIF2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Tgif2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	10
Consensus	ndTGACAKbn
GC content	47.91%
Information content (bits; total / per base)	10.772 / 1.077
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	7627
Previous names	TGIF2.H12RSNP.1.PSM.A

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 (7)	0.682	0.728	0.547	0.617	0.657	0.707	1.705	1.895	75.796	136.229
Mouse	1 (6)	0.919	0.919	0.848	0.87	0.911	0.915	3.236	3.367	96.509	213.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.981	0.969	0.96	0.942	0.928	0.896
Overall, 6 experiments	best	0.988	0.979	0.983	0.972	0.974	0.959
Methyl HT-SELEX, 2 experiments	median	0.982	0.969	0.975	0.958	0.959	0.938
Methyl HT-SELEX, 2 experiments	best	0.984	0.973	0.979	0.964	0.969	0.951
Non-Methyl HT-SELEX, 4 experiments	median	0.968	0.947	0.942	0.915	0.862	0.843
Non-Methyl HT-SELEX, 4 experiments	best	0.988	0.979	0.983	0.972	0.974	0.959

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.85	0.699	0.819	0.596

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	TALE-type HD {3.1.4} (TFClass)
TF subfamily	TGIF {3.1.4.6} (TFClass)
TFClass ID	TFClass: 3.1.4.6.2
HGNC	HGNC:15764
MGI	MGI:1915299
EntrezGene (human)	GeneID:60436 (SSTAR profile)
EntrezGene (mouse)	GeneID:228839 (SSTAR profile)
UniProt ID (human)	TGIF2_HUMAN
UniProt ID (mouse)	TGIF2_MOUSE
UniProt AC (human)	Q9GZN2 (TFClass)
UniProt AC (mouse)	Q8C0Y1 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 1 mouse
HT-SELEX	4
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	TGIF2.H14RSNP.1.PSM.A.pcm
PWM	TGIF2.H14RSNP.1.PSM.A.pwm
PFM	TGIF2.H14RSNP.1.PSM.A.pfm
Threshold to P-value map	TGIF2.H14RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	TGIF2.H14RSNP.1.PSM.A_jaspar_format.txt
MEME format	TGIF2.H14RSNP.1.PSM.A_meme_format.meme
Transfac format	TGIF2.H14RSNP.1.PSM.A_transfac_format.txt
Homer format	TGIF2.H14RSNP.1.PSM.A_homer_format_0.001.txt TGIF2.H14RSNP.1.PSM.A_homer_format_0.0005.txt TGIF2.H14RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1935.25	1898.25	2184.25	1609.25
02	1930.0	1112.0	1391.0	3194.0
03	0.0	0.0	0.0	7627.0
04	0.0	0.0	7627.0	0.0
05	7627.0	0.0	0.0	0.0
06	0.0	7627.0	0.0	0.0
07	7364.0	0.0	263.0	0.0
08	507.0	347.0	5069.0	1704.0
09	680.5	3117.5	2211.5	1617.5
10	1447.25	1994.25	1698.25	2487.25

PFM

	A	C	G	T
01	0.254	0.249	0.286	0.211
02	0.253	0.146	0.182	0.419
03	0.0	0.0	0.0	1.0
04	0.0	0.0	1.0	0.0
05	1.0	0.0	0.0	0.0
06	0.0	1.0	0.0	0.0
07	0.966	0.0	0.034	0.0
08	0.066	0.045	0.665	0.223
09	0.089	0.409	0.29	0.212
10	0.19	0.261	0.223	0.326

PWM

	A	C	G	T
01	0.015	-0.004	0.136	-0.169
02	0.012	-0.538	-0.315	0.515
03	-6.75	-6.75	-6.75	1.385
04	-6.75	-6.75	1.385	-6.75
05	1.385	-6.75	-6.75	-6.75
06	-6.75	1.385	-6.75	-6.75
07	1.35	-6.75	-1.974	-6.75
08	-1.321	-1.699	0.977	-0.112
09	-1.028	0.491	0.148	-0.164
10	-0.275	0.045	-0.116	0.266

Standard thresholds

P-value	Threshold
0.001	4.447245
0.0005	5.96411
0.0001	7.88267