PAX5.H13RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PAX5.H13RSNP.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	19
Consensus	vnbYAnTSAAGCGTGACbn
GC content	54.54%
Information content (bits; total / per base)	18.403 / 0.969
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1958
Previous names	PAX5.H12RSNP.0.PS.A

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)	0.811	0.866	0.733	0.824	0.771	0.846	2.709	3.621	167.592	388.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.999	0.998	0.973	0.971	0.803	0.828
Non-Methyl HT-SELEX, 2 experiments	best	1.0	0.999	0.988	0.987	0.82	0.846

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.754	0.561	0.698	0.444
batch 2	0.562	0.027	0.625	0.422

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	PAX5.H13RSNP.0.PS.A.pcm
PWM	PAX5.H13RSNP.0.PS.A.pwm
PFM	PAX5.H13RSNP.0.PS.A.pfm
Threshold to P-value map	PAX5.H13RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	PAX5.H13RSNP.0.PS.A_jaspar_format.txt
MEME format	PAX5.H13RSNP.0.PS.A_meme_format.meme
Transfac format	PAX5.H13RSNP.0.PS.A_transfac_format.txt
Homer format	PAX5.H13RSNP.0.PS.A_homer_format_0.001.txt PAX5.H13RSNP.0.PS.A_homer_format_0.0005.txt PAX5.H13RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	663.25	277.25	825.25	192.25
02	617.0	431.0	591.0	319.0
03	29.0	642.0	631.0	656.0
04	144.0	1156.0	38.0	620.0
05	1547.0	70.0	295.0	46.0
06	615.0	548.0	478.0	317.0
07	3.0	412.0	21.0	1522.0
08	34.0	1358.0	545.0	21.0
09	1854.0	0.0	104.0	0.0
10	1462.0	37.0	1.0	458.0
11	0.0	277.0	1680.0	1.0
12	0.0	1958.0	0.0	0.0
13	112.0	0.0	1842.0	4.0
14	1.0	1.0	77.0	1879.0
15	289.0	6.0	1649.0	14.0
16	1827.0	18.0	43.0	70.0
17	222.0	1674.0	28.0	34.0
18	150.75	780.75	690.75	335.75
19	568.5	437.5	667.5	284.5

PFM

	A	C	G	T
01	0.339	0.142	0.421	0.098
02	0.315	0.22	0.302	0.163
03	0.015	0.328	0.322	0.335
04	0.074	0.59	0.019	0.317
05	0.79	0.036	0.151	0.023
06	0.314	0.28	0.244	0.162
07	0.002	0.21	0.011	0.777
08	0.017	0.694	0.278	0.011
09	0.947	0.0	0.053	0.0
10	0.747	0.019	0.001	0.234
11	0.0	0.141	0.858	0.001
12	0.0	1.0	0.0	0.0
13	0.057	0.0	0.941	0.002
14	0.001	0.001	0.039	0.96
15	0.148	0.003	0.842	0.007
16	0.933	0.009	0.022	0.036
17	0.113	0.855	0.014	0.017
18	0.077	0.399	0.353	0.171
19	0.29	0.223	0.341	0.145

PWM

	A	C	G	T
01	0.303	-0.566	0.521	-0.929
02	0.231	-0.127	0.188	-0.426
03	-2.767	0.27	0.253	0.292
04	-1.214	0.857	-2.511	0.236
05	1.148	-1.922	-0.504	-2.328
06	0.227	0.112	-0.024	-0.432
07	-4.609	-0.172	-3.066	1.132
08	-2.617	1.018	0.107	-3.066
09	1.329	-5.558	-1.535	-5.558
10	1.092	-2.536	-5.134	-0.066
11	-5.558	-0.566	1.23	-5.134
12	-5.558	1.383	-5.558	-5.558
13	-1.462	-5.558	1.322	-4.423
14	-5.134	-5.134	-1.829	1.342
15	-0.524	-4.131	1.212	-3.431
16	1.314	-3.207	-2.393	-1.922
17	-0.786	1.227	-2.8	-2.617
18	-1.169	0.465	0.343	-0.375
19	0.149	-0.112	0.309	-0.54

Standard thresholds

P-value	Threshold
0.001	0.33566
0.0005	1.88311
0.0001	5.09056