PAX8.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX8.H12INVITRO.0.PSM.A
Gene (human)	PAX8 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Pax8
Gene synonyms (mouse)	Pax-8
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	16
Consensus	YvvTSAWGCGTGACvn
GC content	57.43%
Information content (bits; total / per base)	15.858 / 0.991
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8741

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 (4)	0.717	0.823	0.641	0.769	0.647	0.769	2.391	3.272	41.012	49.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	1.0	1.0	0.998	0.997	0.951	0.953
Overall, 2 experiments	best	1.0	1.0	1.0	1.0	0.998	0.997
Methyl HT-SELEX, 1 experiments	median	1.0	0.999	0.995	0.995	0.904	0.909
Methyl HT-SELEX, 1 experiments	best	1.0	0.999	0.995	0.995	0.904	0.909
Non-Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	1.0	0.998	0.997
Non-Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	0.998	0.997

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.684	0.389	0.678	0.431

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Paired box factors {3.2} (TFClass)
TF family	PD {3.2.2} (TFClass)
TF subfamily	PAX2-like {3.2.2.2} (TFClass)
TFClass ID	TFClass: 3.2.2.2.3
HGNC	HGNC:8622
MGI	MGI:97492
EntrezGene (human)	GeneID:7849 (SSTAR profile)
EntrezGene (mouse)	GeneID:18510 (SSTAR profile)
UniProt ID (human)	PAX8_HUMAN
UniProt ID (mouse)	PAX8_MOUSE
UniProt AC (human)	Q06710 (TFClass)
UniProt AC (mouse)	Q00288 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	PAX8.H12INVITRO.0.PSM.A.pcm
PWM	PAX8.H12INVITRO.0.PSM.A.pwm
PFM	PAX8.H12INVITRO.0.PSM.A.pfm
Alignment	PAX8.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	PAX8.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	PAX8.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	PAX8.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	PAX8.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	PAX8.H12INVITRO.0.PSM.A_homer_format_0.001.txt PAX8.H12INVITRO.0.PSM.A_homer_format_0.0005.txt PAX8.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	790.5	5418.5	659.5	1872.5
02	3958.5	786.5	3325.5	670.5
03	1517.0	3994.0	2047.0	1183.0
04	36.0	1199.0	86.0	7420.0
05	249.0	5813.0	2557.0	122.0
06	7700.0	20.0	974.0	47.0
07	5589.0	159.0	156.0	2837.0
08	4.0	1072.0	7662.0	3.0
09	10.0	8705.0	8.0	18.0
10	682.0	8.0	8026.0	25.0
11	44.0	883.0	435.0	7379.0
12	1489.0	58.0	7029.0	165.0
13	7966.0	129.0	212.0	434.0
14	774.0	7718.0	96.0	153.0
15	1016.25	3396.25	3350.25	978.25
16	2510.25	1599.25	2735.25	1896.25

PFM

	A	C	G	T
01	0.09	0.62	0.075	0.214
02	0.453	0.09	0.38	0.077
03	0.174	0.457	0.234	0.135
04	0.004	0.137	0.01	0.849
05	0.028	0.665	0.293	0.014
06	0.881	0.002	0.111	0.005
07	0.639	0.018	0.018	0.325
08	0.0	0.123	0.877	0.0
09	0.001	0.996	0.001	0.002
10	0.078	0.001	0.918	0.003
11	0.005	0.101	0.05	0.844
12	0.17	0.007	0.804	0.019
13	0.911	0.015	0.024	0.05
14	0.089	0.883	0.011	0.018
15	0.116	0.389	0.383	0.112
16	0.287	0.183	0.313	0.217

PWM

	A	C	G	T
01	-1.015	0.907	-1.196	-0.154
02	0.594	-1.02	0.42	-1.179
03	-0.365	0.603	-0.065	-0.613
04	-4.046	-0.599	-3.21	1.222
05	-2.164	0.978	0.157	-2.868
06	1.259	-4.587	-0.807	-3.793
07	0.938	-2.607	-2.626	0.261
08	-5.855	-0.711	1.254	-6.029
09	-5.183	1.381	-5.361	-4.681
10	-1.162	-5.361	1.3	-4.385
11	-3.856	-0.905	-1.61	1.216
12	-0.383	-3.592	1.168	-2.571
13	1.293	-2.813	-2.323	-1.612
14	-1.036	1.261	-3.103	-2.645
15	-0.764	0.441	0.427	-0.802
16	0.139	-0.312	0.224	-0.142

Standard thresholds

P-value	Threshold
0.001	2.19821
0.0005	3.51836
0.0001	6.23311