TGIF2.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TGIF2.H12INVIVO.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	11
Consensus	dbTGACAGvhv
GC content	50.74%
Information content (bits; total / per base)	11.383 / 1.035
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	239

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)	0.704	0.747	0.569	0.618	0.66	0.713	1.869	2.045	80.071	125.77
Mouse	1 (6)	0.928	0.932	0.868	0.882	0.916	0.919	3.578	3.639	104.721	225.009

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.977	0.96	0.956	0.936	0.909	0.876
Overall, 6 experiments	best	0.987	0.978	0.982	0.969	0.97	0.954
Methyl HT-SELEX, 2 experiments	median	0.977	0.96	0.971	0.951	0.951	0.928
Methyl HT-SELEX, 2 experiments	best	0.983	0.971	0.977	0.961	0.963	0.944
Non-Methyl HT-SELEX, 4 experiments	median	0.966	0.945	0.937	0.91	0.842	0.826
Non-Methyl HT-SELEX, 4 experiments	best	0.987	0.978	0.982	0.969	0.97	0.954

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.821	0.679	0.76	0.545

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.H12INVIVO.1.PSM.A.pcm
PWM	TGIF2.H12INVIVO.1.PSM.A.pwm
PFM	TGIF2.H12INVIVO.1.PSM.A.pfm
Alignment	TGIF2.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	TGIF2.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	TGIF2.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	TGIF2.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	TGIF2.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	TGIF2.H12INVIVO.1.PSM.A_homer_format_0.001.txt TGIF2.H12INVIVO.1.PSM.A_homer_format_0.0005.txt TGIF2.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	68.0	31.0	53.0	87.0
02	26.0	62.0	55.0	96.0
03	0.0	1.0	2.0	236.0
04	1.0	3.0	235.0	0.0
05	233.0	0.0	5.0	1.0
06	1.0	238.0	0.0	0.0
07	234.0	0.0	2.0	3.0
08	24.0	11.0	200.0	4.0
09	29.0	113.0	73.0	24.0
10	49.0	59.0	25.0	106.0
11	51.0	53.0	113.0	22.0

PFM

	A	C	G	T
01	0.285	0.13	0.222	0.364
02	0.109	0.259	0.23	0.402
03	0.0	0.004	0.008	0.987
04	0.004	0.013	0.983	0.0
05	0.975	0.0	0.021	0.004
06	0.004	0.996	0.0	0.0
07	0.979	0.0	0.008	0.013
08	0.1	0.046	0.837	0.017
09	0.121	0.473	0.305	0.1
10	0.205	0.247	0.105	0.444
11	0.213	0.222	0.473	0.092

PWM

	A	C	G	T
01	0.127	-0.636	-0.117	0.369
02	-0.803	0.036	-0.081	0.466
03	-3.799	-3.25	-2.898	1.357
04	-3.25	-2.638	1.353	-3.799
05	1.344	-3.799	-2.261	-3.25
06	-3.25	1.365	-3.799	-3.799
07	1.348	-3.799	-2.898	-2.638
08	-0.879	-1.598	1.192	-2.432
09	-0.699	0.627	0.196	-0.879
10	-0.193	-0.012	-0.841	0.563
11	-0.155	-0.117	0.627	-0.961

Standard thresholds

P-value	Threshold
0.001	4.358095
0.0005	5.309205
0.0001	7.667465