GATA5.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GATA5.H12INVIVO.0.SM.D
Gene (human)	GATA5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Gata5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	10
Consensus	nhGATAAvnn
GC content	34.98%
Information content (bits; total / per base)	10.535 / 1.053
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8780

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.989	0.981	0.986	0.976	0.982	0.97
Overall, 6 experiments	best	0.996	0.994	0.994	0.99	0.991	0.985
Methyl HT-SELEX, 2 experiments	median	0.994	0.99	0.99	0.984	0.985	0.976
Methyl HT-SELEX, 2 experiments	best	0.995	0.992	0.992	0.987	0.987	0.979
Non-Methyl HT-SELEX, 4 experiments	median	0.984	0.973	0.979	0.964	0.931	0.921
Non-Methyl HT-SELEX, 4 experiments	best	0.996	0.994	0.994	0.99	0.991	0.985

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.967	0.837	0.923	0.615
batch 2	0.825	0.548	0.804	0.599

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: 2.2.1.1.5
HGNC	HGNC:15802
MGI	MGI:109497
EntrezGene (human)	GeneID:140628 (SSTAR profile)
EntrezGene (mouse)	GeneID:14464 (SSTAR profile)
UniProt ID (human)	GATA5_HUMAN
UniProt ID (mouse)	GATA5_MOUSE
UniProt AC (human)	Q9BWX5 (TFClass)
UniProt AC (mouse)	P97489 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	GATA5.H12INVIVO.0.SM.D.pcm
PWM	GATA5.H12INVIVO.0.SM.D.pwm
PFM	GATA5.H12INVIVO.0.SM.D.pfm
Alignment	GATA5.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	GATA5.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	GATA5.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	GATA5.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	GATA5.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	GATA5.H12INVIVO.0.SM.D_homer_format_0.001.txt GATA5.H12INVIVO.0.SM.D_homer_format_0.0005.txt GATA5.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2341.75	2070.75	2817.75	1549.75
02	3755.25	1531.25	772.25	2721.25
03	0.0	0.0	8780.0	0.0
04	8780.0	0.0	0.0	0.0
05	0.0	0.0	0.0	8780.0
06	8780.0	0.0	0.0	0.0
07	8780.0	0.0	0.0	0.0
08	1423.0	2383.0	4006.0	968.0
09	3013.75	2166.75	2475.75	1123.75
10	2854.5	1895.5	1817.5	2212.5

PFM

	A	C	G	T
01	0.267	0.236	0.321	0.177
02	0.428	0.174	0.088	0.31
03	0.0	0.0	1.0	0.0
04	1.0	0.0	0.0	0.0
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.162	0.271	0.456	0.11
09	0.343	0.247	0.282	0.128
10	0.325	0.216	0.207	0.252

PWM

	A	C	G	T
01	0.065	-0.058	0.25	-0.348
02	0.537	-0.36	-1.043	0.215
03	-6.875	-6.875	1.386	-6.875
04	1.386	-6.875	-6.875	-6.875
05	-6.875	-6.875	-6.875	1.386
06	1.386	-6.875	-6.875	-6.875
07	1.386	-6.875	-6.875	-6.875
08	-0.433	0.082	0.601	-0.817
09	0.317	-0.013	0.12	-0.669
10	0.262	-0.147	-0.189	0.008

Standard thresholds

P-value	Threshold
0.001	0.453125
0.0005	6.52178
0.0001	7.73902