GFI1.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	GFI1.H12INVIVO.0.PSM.A
Gene (human)	GFI1 (GeneCards)
Gene synonyms (human)	ZNF163
Gene (mouse)	Gfi1
Gene synonyms (mouse)	Gfi-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	10
Consensus	RCWSWGATTK
GC content	39.9%
Information content (bits; total / per base)	11.514 / 1.151
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	998

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	3 (15)	0.843	0.916	0.782	0.853	0.846	0.904	3.317	3.532	131.745	315.638
Mouse	5 (31)	0.768	0.916	0.661	0.843	0.777	0.903	2.592	3.45	103.495	320.161

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.999	0.997	0.998	0.996	0.993	0.99
Overall, 2 experiments	best	0.999	0.998	0.998	0.996	0.993	0.99
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.998	0.996	0.992	0.99
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.998	0.996	0.992	0.99
Non-Methyl HT-SELEX, 1 experiments	median	0.998	0.997	0.998	0.996	0.993	0.99
Non-Methyl HT-SELEX, 1 experiments	best	0.998	0.997	0.998	0.996	0.993	0.99

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.791	0.536	0.777	0.59

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	More than 3 adjacent zinc fingers {2.3.3} (TFClass)
TF subfamily	GFI1 {2.3.3.21} (TFClass)
TFClass ID	TFClass: 2.3.3.21.1
HGNC	HGNC:4237
MGI	MGI:103170
EntrezGene (human)	GeneID:2672 (SSTAR profile)
EntrezGene (mouse)	GeneID:14581 (SSTAR profile)
UniProt ID (human)	GFI1_HUMAN
UniProt ID (mouse)	GFI1_MOUSE
UniProt AC (human)	Q99684 (TFClass)
UniProt AC (mouse)	P70338 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 5 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	GFI1.H12INVIVO.0.PSM.A.pcm
PWM	GFI1.H12INVIVO.0.PSM.A.pwm
PFM	GFI1.H12INVIVO.0.PSM.A.pfm
Alignment	GFI1.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	GFI1.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	GFI1.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	GFI1.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	GFI1.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	GFI1.H12INVIVO.0.PSM.A_homer_format_0.001.txt GFI1.H12INVIVO.0.PSM.A_homer_format_0.0005.txt GFI1.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	163.0	83.0	635.0	117.0
02	67.0	820.0	29.0	82.0
03	339.0	120.0	7.0	532.0
04	9.0	315.0	579.0	95.0
05	358.0	3.0	7.0	630.0
06	1.0	5.0	990.0	2.0
07	891.0	20.0	84.0	3.0
08	1.0	16.0	8.0	973.0
09	1.0	1.0	4.0	992.0
10	43.0	96.0	160.0	699.0

PFM

	A	C	G	T
01	0.163	0.083	0.636	0.117
02	0.067	0.822	0.029	0.082
03	0.34	0.12	0.007	0.533
04	0.009	0.316	0.58	0.095
05	0.359	0.003	0.007	0.631
06	0.001	0.005	0.992	0.002
07	0.893	0.02	0.084	0.003
08	0.001	0.016	0.008	0.975
09	0.001	0.001	0.004	0.994
10	0.043	0.096	0.16	0.7

PWM

	A	C	G	T
01	-0.422	-1.087	0.93	-0.75
02	-1.296	1.185	-2.101	-1.099
03	0.305	-0.725	-3.36	0.754
04	-3.154	0.232	0.838	-0.954
05	0.359	-3.973	-3.36	0.922
06	-4.523	-3.62	1.373	-4.211
07	1.268	-2.448	-1.075	-3.973
08	-4.523	-2.651	-3.252	1.356
09	-4.523	-4.523	-3.781	1.375
10	-1.726	-0.944	-0.44	1.026

Standard thresholds

P-value	Threshold
0.001	4.28026
0.0005	5.316005
0.0001	7.37755