TGIF2.H12INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TGIF2.H12INVITRO.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	8
Consensus	nTGACAbn
GC content	46.61%
Information content (bits; total / per base)	10.422 / 1.303
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9360

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)	0.671	0.738	0.546	0.618	0.65	0.715	1.638	1.834	64.071	121.301
Mouse	1 (6)	0.903	0.904	0.824	0.844	0.901	0.904	2.961	3.02	85.337	201.481

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.985	0.976	0.972	0.96	0.926	0.897
Overall, 6 experiments	best	0.997	0.997	0.984	0.975	0.974	0.961
Methyl HT-SELEX, 2 experiments	median	0.985	0.977	0.977	0.964	0.962	0.944
Methyl HT-SELEX, 2 experiments	best	0.991	0.988	0.983	0.975	0.974	0.961
Non-Methyl HT-SELEX, 4 experiments	median	0.973	0.958	0.957	0.937	0.873	0.86
Non-Methyl HT-SELEX, 4 experiments	best	0.997	0.997	0.984	0.975	0.974	0.961

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.832	0.655	0.793	0.564

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

PCM	TGIF2.H12INVITRO.1.PSM.A.pcm
PWM	TGIF2.H12INVITRO.1.PSM.A.pwm
PFM	TGIF2.H12INVITRO.1.PSM.A.pfm
Alignment	TGIF2.H12INVITRO.1.PSM.A.words.tsv
Threshold to P-value map	TGIF2.H12INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	TGIF2.H12INVITRO.1.PSM.A_jaspar_format.txt
MEME format	TGIF2.H12INVITRO.1.PSM.A_meme_format.meme
Transfac format	TGIF2.H12INVITRO.1.PSM.A_transfac_format.txt
Homer format	TGIF2.H12INVITRO.1.PSM.A_homer_format_0.001.txt TGIF2.H12INVITRO.1.PSM.A_homer_format_0.0005.txt TGIF2.H12INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2474.25	1749.25	2009.25	3127.25
02	16.0	35.0	4.0	9305.0
03	0.0	0.0	9360.0	0.0
04	9360.0	0.0	0.0	0.0
05	0.0	9360.0	0.0	0.0
06	9360.0	0.0	0.0	0.0
07	922.0	1077.0	5362.0	1999.0
08	1284.75	3087.75	2856.75	2130.75

PFM

	A	C	G	T
01	0.264	0.187	0.215	0.334
02	0.002	0.004	0.0	0.994
03	0.0	0.0	1.0	0.0
04	1.0	0.0	0.0	0.0
05	0.0	1.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.099	0.115	0.573	0.214
08	0.137	0.33	0.305	0.228

PWM

	A	C	G	T
01	0.056	-0.291	-0.152	0.29
02	-4.853	-4.14	-5.921	1.38
03	-6.932	-6.932	1.386	-6.932
04	1.386	-6.932	-6.932	-6.932
05	-6.932	1.386	-6.932	-6.932
06	1.386	-6.932	-6.932	-6.932
07	-0.93	-0.775	0.829	-0.157
08	-0.599	0.277	0.199	-0.094

Standard thresholds

P-value	Threshold
0.001	2.65365
0.0005	6.433085
0.0001	7.77457