PAX5.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX5.H12INVIVO.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	20
Consensus	nvdRnbCRvYSRdGCRKRRM
GC content	59.78%
Information content (bits; total / per base)	11.331 / 0.567
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000

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)	0.855	0.924	0.763	0.876	0.867	0.923	3.554	4.969	177.938	506.149

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.999	0.999	0.997	0.996	0.936	0.94
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.999	0.999	0.968	0.97

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.72	0.508	0.694	0.446
batch 2	0.545	0.02	0.594	0.2

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.H12INVIVO.0.PS.A.pcm
PWM	PAX5.H12INVIVO.0.PS.A.pwm
PFM	PAX5.H12INVIVO.0.PS.A.pfm
Alignment	PAX5.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	PAX5.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	PAX5.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	PAX5.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	PAX5.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	PAX5.H12INVIVO.0.PS.A_homer_format_0.001.txt PAX5.H12INVIVO.0.PS.A_homer_format_0.0005.txt PAX5.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	164.0	370.0	252.0	214.0
02	270.0	234.0	387.0	109.0
03	278.0	106.0	311.0	305.0
04	328.0	54.0	594.0	24.0
05	228.0	203.0	379.0	190.0
06	15.0	224.0	479.0	282.0
07	53.0	788.0	14.0	145.0
08	733.0	68.0	144.0	55.0
09	171.0	233.0	501.0	95.0
10	31.0	514.0	97.0	358.0
11	149.0	448.0	380.0	23.0
12	586.0	30.0	371.0	13.0
13	518.0	59.0	203.0	220.0
14	1.0	292.0	697.0	10.0
15	13.0	812.0	21.0	154.0
16	266.0	29.0	666.0	39.0
17	91.0	50.0	240.0	619.0
18	286.0	29.0	678.0	7.0
19	666.0	53.0	197.0	84.0
20	224.0	707.0	42.0	27.0

PFM

	A	C	G	T
01	0.164	0.37	0.252	0.214
02	0.27	0.234	0.387	0.109
03	0.278	0.106	0.311	0.305
04	0.328	0.054	0.594	0.024
05	0.228	0.203	0.379	0.19
06	0.015	0.224	0.479	0.282
07	0.053	0.788	0.014	0.145
08	0.733	0.068	0.144	0.055
09	0.171	0.233	0.501	0.095
10	0.031	0.514	0.097	0.358
11	0.149	0.448	0.38	0.023
12	0.586	0.03	0.371	0.013
13	0.518	0.059	0.203	0.22
14	0.001	0.292	0.697	0.01
15	0.013	0.812	0.021	0.154
16	0.266	0.029	0.666	0.039
17	0.091	0.05	0.24	0.619
18	0.286	0.029	0.678	0.007
19	0.666	0.053	0.197	0.084
20	0.224	0.707	0.042	0.027

PWM

	A	C	G	T
01	-0.418	0.39	0.008	-0.154
02	0.076	-0.066	0.435	-0.821
03	0.105	-0.849	0.217	0.198
04	0.27	-1.508	0.861	-2.281
05	-0.091	-0.207	0.414	-0.272
06	-2.711	-0.109	0.647	0.12
07	-1.526	1.143	-2.773	-0.54
08	1.071	-1.284	-0.547	-1.49
09	-0.377	-0.07	0.692	-0.956
10	-2.04	0.717	-0.936	0.357
11	-0.513	0.58	0.416	-2.32
12	0.848	-2.071	0.393	-2.839
13	0.725	-1.422	-0.207	-0.127
14	-4.525	0.154	1.021	-3.066
15	-2.839	1.173	-2.405	-0.48
16	0.062	-2.103	0.976	-1.821
17	-0.999	-1.582	-0.041	0.903
18	0.134	-2.103	0.993	-3.362
19	0.976	-1.526	-0.236	-1.077
20	-0.109	1.035	-1.75	-2.171

Standard thresholds

P-value	Threshold
0.001	4.43956
0.0005	5.32226
0.0001	7.14796