GATA3.H12RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GATA3.H12RSNP.1.SM.B
Gene (human)	GATA3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Gata3
Gene synonyms (mouse)	Gata-3
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	11
Consensus	nvAGATAAGRW
GC content	30.75%
Information content (bits; total / per base)	14.816 / 1.347
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	436

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	54 (340)	0.662	0.835	0.554	0.773	0.716	0.89	1.969	3.18	87.953	250.745
Mouse	29 (173)	0.687	0.759	0.594	0.683	0.711	0.766	2.064	2.363	121.886	309.538

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.849	0.82	0.7	0.696	0.593	0.615
Overall, 6 experiments	best	0.992	0.987	0.988	0.98	0.983	0.973
Methyl HT-SELEX, 1 experiments	median	0.992	0.987	0.988	0.98	0.983	0.973
Methyl HT-SELEX, 1 experiments	best	0.992	0.987	0.988	0.98	0.983	0.973
Non-Methyl HT-SELEX, 5 experiments	median	0.848	0.815	0.691	0.694	0.585	0.611
Non-Methyl HT-SELEX, 5 experiments	best	0.987	0.978	0.983	0.971	0.975	0.96

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.259	6.056	0.173	0.109

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.899	0.24	0.895	0.496
batch 2	0.638	0.269	0.622	0.448

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Other C4 zinc finger-type factors {2.2} (TFClass)
TF family	C4-GATA-related {2.2.1} (TFClass)
TF subfamily	GATA double {2.2.1.1} (TFClass)
TFClass ID	TFClass: 2.2.1.1.3
HGNC	HGNC:4172
MGI	MGI:95663
EntrezGene (human)	GeneID:2625 (SSTAR profile)
EntrezGene (mouse)	GeneID:14462 (SSTAR profile)
UniProt ID (human)	GATA3_HUMAN
UniProt ID (mouse)	GATA3_MOUSE
UniProt AC (human)	P23771 (TFClass)
UniProt AC (mouse)	P23772 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	54 human, 29 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	GATA3.H12RSNP.1.SM.B.pcm
PWM	GATA3.H12RSNP.1.SM.B.pwm
PFM	GATA3.H12RSNP.1.SM.B.pfm
Alignment	GATA3.H12RSNP.1.SM.B.words.tsv
Threshold to P-value map	GATA3.H12RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	GATA3.H12RSNP.1.SM.B_jaspar_format.txt
MEME format	GATA3.H12RSNP.1.SM.B_meme_format.meme
Transfac format	GATA3.H12RSNP.1.SM.B_transfac_format.txt
Homer format	GATA3.H12RSNP.1.SM.B_homer_format_0.001.txt GATA3.H12RSNP.1.SM.B_homer_format_0.0005.txt GATA3.H12RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	110.5	72.5	83.5	169.5
02	148.0	191.0	64.0	33.0
03	372.0	0.0	0.0	64.0
04	0.0	0.0	436.0	0.0
05	436.0	0.0	0.0	0.0
06	0.0	0.0	0.0	436.0
07	436.0	0.0	0.0	0.0
08	436.0	0.0	0.0	0.0
09	0.0	31.0	405.0	0.0
10	321.0	51.0	56.0	8.0
11	50.0	39.0	46.0	301.0

PFM

	A	C	G	T
01	0.253	0.166	0.192	0.389
02	0.339	0.438	0.147	0.076
03	0.853	0.0	0.0	0.147
04	0.0	0.0	1.0	0.0
05	1.0	0.0	0.0	0.0
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	0.071	0.929	0.0
10	0.736	0.117	0.128	0.018
11	0.115	0.089	0.106	0.69

PWM

	A	C	G	T
01	0.013	-0.401	-0.262	0.437
02	0.302	0.555	-0.523	-1.164
03	1.218	-4.287	-4.287	-0.523
04	-4.287	-4.287	1.376	-4.287
05	1.376	-4.287	-4.287	-4.287
06	-4.287	-4.287	-4.287	1.376
07	1.376	-4.287	-4.287	-4.287
08	1.376	-4.287	-4.287	-4.287
09	-4.287	-1.223	1.302	-4.287
10	1.071	-0.744	-0.653	-2.452
11	-0.763	-1.003	-0.844	1.007

Standard thresholds

P-value	Threshold
0.001	2.50816
0.0005	3.873205
0.0001	6.548225