NACC2.H13INVITRO.0.PSGIB.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NACC2.H13INVITRO.0.PSGIB.A
Gene (human)	NACC2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Nacc2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	10
Consensus	nWCATGYddn
GC content	40.24%
Information content (bits; total / per base)	7.626 / 0.763
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX + SMiLe-Seq + PBM
Aligned words	616
Previous names

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	Centrality, median	Centrality, best
Overall	3 (3)	0.871	0.873	0.719	0.732	0.464	0.534	32.699	53.119

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
overall, 4 experiments	median	0.804	0.78	0.687	0.677	0.605	0.611
overall, 4 experiments	best	0.998	0.997	0.993	0.991	0.981	0.975
Lysate, 1 experiments	median	0.888	0.869	0.737	0.733	0.635	0.647
Lysate, 1 experiments	best	0.888	0.869	0.737	0.733	0.635	0.647
IVT, 2 experiments	median	0.651	0.618	0.601	0.58	0.561	0.553
IVT, 2 experiments	best	0.719	0.69	0.637	0.62	0.576	0.576
GFPIVT, 1 experiments	median	0.998	0.997	0.993	0.991	0.981	0.975
GFPIVT, 1 experiments	best	0.998	0.997	0.993	0.991	0.981	0.975

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
overall, 2 experiments	median	75.854	0.488	0.883	0.699
overall, 2 experiments	best	154.721	0.55	0.924	0.78
Lysate, 1 experiments	median	146.456	0.451	0.923	0.78
Lysate, 1 experiments	best	146.456	0.451	0.923	0.78
GFPIVT, 1 experiments	median	49.116	0.509	0.828	0.65
GFPIVT, 1 experiments	best	154.721	0.55	0.924	0.764

SMiLE-Seq benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.867	0.841	0.808	0.787	0.756	0.739
Overall, 2 experiments	best	0.978	0.969	0.954	0.934	0.912	0.886

PBM benchmarking		auROC, QNZS	auPR, QNZS	auROC, SD	auPR, SD
Overall, 3 experiments	median	0.953	0.112	0.891	0.14
Overall, 3 experiments	best	0.953	0.112	0.955	0.172

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Other {3.0} (TFClass)
TF family	BEN {3.0.257} (TFClass)
TF subfamily	{3.0.257.0} (TFClass)
TFClass ID	TFClass: 3.0.257.0.1
HGNC
MGI
EntrezGene (human)
EntrezGene (mouse)
UniProt ID (human)	NACC2_HUMAN
UniProt ID (mouse)	NACC2_MOUSE
UniProt AC (human)	Q96BF6 (TFClass)
UniProt AC (mouse)	Q9DCM7 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 0 mouse
HT-SELEX	4 overall: 1 Lysate, 2 IVT, 1 GFPIVT
Genomic HT-SELEX	2 overall: 1 Lysate, 0 IVT, 1 GFPIVT
SMiLE-Seq	2
PBM	3

PCM	NACC2.H13INVITRO.0.PSGIB.A.pcm
PWM	NACC2.H13INVITRO.0.PSGIB.A.pwm
PFM	NACC2.H13INVITRO.0.PSGIB.A.pfm
Threshold to P-value map	NACC2.H13INVITRO.0.PSGIB.A.thr
Motif in other formats
JASPAR format	NACC2.H13INVITRO.0.PSGIB.A_jaspar_format.txt
MEME format	NACC2.H13INVITRO.0.PSGIB.A_meme_format.meme
Transfac format	NACC2.H13INVITRO.0.PSGIB.A_transfac_format.txt
Homer format	NACC2.H13INVITRO.0.PSGIB.A_homer_format_0.001.txt NACC2.H13INVITRO.0.PSGIB.A_homer_format_0.0005.txt NACC2.H13INVITRO.0.PSGIB.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	179.0	121.0	161.0	155.0
02	390.0	53.0	8.0	165.0
03	4.0	606.0	6.0	0.0
04	616.0	0.0	0.0	0.0
05	17.0	108.0	0.0	491.0
06	287.0	0.0	329.0	0.0
07	0.0	277.0	86.0	253.0
08	184.0	69.0	212.0	151.0
09	280.0	62.0	87.0	187.0
10	183.0	169.0	125.0	139.0

PFM

	A	C	G	T
01	0.291	0.196	0.261	0.252
02	0.633	0.086	0.013	0.268
03	0.006	0.984	0.01	0.0
04	1.0	0.0	0.0	0.0
05	0.028	0.175	0.0	0.797
06	0.466	0.0	0.534	0.0
07	0.0	0.45	0.14	0.411
08	0.299	0.112	0.344	0.245
09	0.455	0.101	0.141	0.304
10	0.297	0.274	0.203	0.226

PWM

	A	C	G	T
01	0.149	-0.238	0.044	0.006
02	0.923	-1.047	-2.785	0.068
03	-3.324	1.362	-3.018	-4.574
04	1.379	-4.574	-4.574	-4.574
05	-2.124	-0.35	-4.574	1.152
06	0.618	-4.574	0.754	-4.574
07	-4.574	0.582	-0.574	0.492
08	0.176	-0.79	0.317	-0.019
09	0.593	-0.895	-0.563	0.192
10	0.171	0.092	-0.206	-0.101

Standard thresholds

P-value	Threshold
0.001	5.503095
0.0005	5.94666
0.0001	6.77444