PAX5.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX5.H12INVITRO.0.PS.A
Gene (human)	PAX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Pax5
Gene synonyms (mouse)	Pax-5
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	18
Consensus	nRnbYAnTSAWGCGTGWM
GC content	52.02%
Information content (bits; total / per base)	15.99 / 0.888
Data sources	ChIP-Seq + HT-SELEX
Aligned words	7536

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	12 (80)	0.83	0.893	0.741	0.842	0.764	0.833	2.604	3.551	161.57	383.481

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.999	0.999	0.998	0.997	0.947	0.95
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	1.0	0.999	0.975	0.976

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.733	0.533	0.676	0.432
batch 2	0.626	0.03	0.672	0.378

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: 3.2.2.2.2
HGNC	HGNC:8619
MGI	MGI:97489
EntrezGene (human)	GeneID:5079 (SSTAR profile)
EntrezGene (mouse)	GeneID:18507 (SSTAR profile)
UniProt ID (human)	PAX5_HUMAN
UniProt ID (mouse)	PAX5_MOUSE
UniProt AC (human)	Q02548 (TFClass)
UniProt AC (mouse)	Q02650 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	12 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	PAX5.H12INVITRO.0.PS.A.pcm
PWM	PAX5.H12INVITRO.0.PS.A.pwm
PFM	PAX5.H12INVITRO.0.PS.A.pfm
Alignment	PAX5.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	PAX5.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	PAX5.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	PAX5.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	PAX5.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	PAX5.H12INVITRO.0.PS.A_homer_format_0.001.txt PAX5.H12INVITRO.0.PS.A_homer_format_0.0005.txt PAX5.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1939.75	1368.75	1905.75	2321.75
02	3187.75	591.75	3391.75	364.75
03	2784.0	1585.0	2040.0	1127.0
04	116.0	2268.0	1991.0	3161.0
05	437.0	4682.0	96.0	2321.0
06	6071.0	228.0	1102.0	135.0
07	2248.0	2027.0	2059.0	1202.0
08	13.0	1697.0	56.0	5770.0
09	127.0	5275.0	2078.0	56.0
10	7113.0	1.0	412.0	10.0
11	5140.0	386.0	34.0	1976.0
12	0.0	1491.0	6045.0	0.0
13	1.0	7511.0	21.0	3.0
14	1058.0	5.0	6316.0	157.0
15	75.0	59.0	232.0	7170.0
16	1031.0	38.0	6365.0	102.0
17	5038.25	681.25	854.25	962.25
18	1170.25	4958.25	706.25	701.25

PFM

	A	C	G	T
01	0.257	0.182	0.253	0.308
02	0.423	0.079	0.45	0.048
03	0.369	0.21	0.271	0.15
04	0.015	0.301	0.264	0.419
05	0.058	0.621	0.013	0.308
06	0.806	0.03	0.146	0.018
07	0.298	0.269	0.273	0.16
08	0.002	0.225	0.007	0.766
09	0.017	0.7	0.276	0.007
10	0.944	0.0	0.055	0.001
11	0.682	0.051	0.005	0.262
12	0.0	0.198	0.802	0.0
13	0.0	0.997	0.003	0.0
14	0.14	0.001	0.838	0.021
15	0.01	0.008	0.031	0.951
16	0.137	0.005	0.845	0.014
17	0.669	0.09	0.113	0.128
18	0.155	0.658	0.094	0.093

PWM

	A	C	G	T
01	0.029	-0.319	0.011	0.209
02	0.525	-1.155	0.587	-1.637
03	0.39	-0.173	0.079	-0.513
04	-2.77	0.185	0.055	0.517
05	-1.457	0.91	-2.955	0.208
06	1.169	-2.103	-0.535	-2.621
07	0.176	0.073	0.089	-0.449
08	-4.819	-0.104	-3.478	1.118
09	-2.681	1.029	0.098	-3.478
10	1.328	-6.369	-1.516	-5.038
11	1.003	-1.581	-3.952	0.048
12	-6.74	-0.234	1.165	-6.74
13	-6.369	1.382	-4.397	-5.888
14	-0.576	-5.564	1.209	-2.472
15	-3.196	-3.428	-2.086	1.336
16	-0.602	-3.848	1.217	-2.896
17	0.983	-1.015	-0.79	-0.671
18	-0.475	0.967	-0.979	-0.986

Standard thresholds

P-value	Threshold
0.001	1.98071
0.0005	3.36441
0.0001	6.18401