JRK.H13CORE.0.PSGB.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	JRK.H13CORE.0.PSGB.A
Gene (human)	JRK (GeneCards)
Gene synonyms (human)
Gene (mouse)	Jrk
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	19
Consensus	nvCCTCRvTTAACCGGAAh
GC content	49.55%
Information content (bits; total / per base)	25.894 / 1.363
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX + PBM
Aligned words	9931
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 (4)	0.816	0.848	0.773	0.796	0.693	0.725	63.26	74.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
overall, 5 experiments	median	1.0	1.0	1.0	1.0	0.868	0.89
overall, 5 experiments	best	1.0	1.0	1.0	1.0	0.997	0.997
Lysate, 2 experiments	median	1.0	1.0	1.0	1.0	0.981	0.982
Lysate, 2 experiments	best	1.0	1.0	1.0	1.0	0.997	0.997
IVT, 1 experiments	median	0.931	0.934	0.708	0.741	0.589	0.635
IVT, 1 experiments	best	0.931	0.934	0.708	0.741	0.589	0.635
GFPIVT, 2 experiments	median	1.0	1.0	0.948	0.954	0.789	0.82
GFPIVT, 2 experiments	best	1.0	1.0	1.0	1.0	0.868	0.89

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
overall, 4 experiments	median	191.044	0.797	0.808	0.828
overall, 4 experiments	best	679.854	0.97	0.972	0.967
Lysate, 2 experiments	median	609.72	0.937	0.958	0.954
Lysate, 2 experiments	best	679.854	0.97	0.972	0.967
GFPIVT, 2 experiments	median	139.159	0.737	0.753	0.778
GFPIVT, 2 experiments	best	213.022	0.831	0.842	0.86

PBM benchmarking		auROC, QNZS	auPR, QNZS	auROC, SD	auPR, SD
Overall, 6 experiments	median	0.792	0.026	0.679	0.016
Overall, 6 experiments	best	0.797	0.088	0.751	0.047

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Other {3.0} (TFClass)
TF family	CENPB {3.0.256} (TFClass)
TF subfamily	{3.0.256.0} (TFClass)
TFClass ID	TFClass: 3.0.256.0.1
HGNC
MGI
EntrezGene (human)
EntrezGene (mouse)
UniProt ID (human)	JERKY_HUMAN
UniProt ID (mouse)	JERKY_MOUSE
UniProt AC (human)	O75564 (TFClass)
UniProt AC (mouse)	Q60976 (TFClass)
GRECO-DB-TF	no

ChIP-Seq	3 human, 0 mouse
HT-SELEX	5 overall: 2 Lysate, 1 IVT, 2 GFPIVT
Genomic HT-SELEX	4 overall: 2 Lysate, 0 IVT, 2 GFPIVT
SMiLE-Seq	0
PBM	6

PCM	JRK.H13CORE.0.PSGB.A.pcm
PWM	JRK.H13CORE.0.PSGB.A.pwm
PFM	JRK.H13CORE.0.PSGB.A.pfm
Threshold to P-value map	JRK.H13CORE.0.PSGB.A.thr
Motif in other formats
JASPAR format	JRK.H13CORE.0.PSGB.A_jaspar_format.txt
MEME format	JRK.H13CORE.0.PSGB.A_meme_format.meme
Transfac format	JRK.H13CORE.0.PSGB.A_transfac_format.txt
Homer format	JRK.H13CORE.0.PSGB.A_homer_format_0.001.txt JRK.H13CORE.0.PSGB.A_homer_format_0.0005.txt JRK.H13CORE.0.PSGB.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3771.75	2690.75	1775.75	1692.75
02	4582.25	2315.25	2728.25	305.25
03	287.0	9411.0	85.0	148.0
04	31.0	9174.0	9.0	717.0
05	11.0	1383.0	9.0	8528.0
06	13.0	9895.0	7.0	16.0
07	4761.0	70.0	5052.0	48.0
08	3460.0	1743.0	3636.0	1092.0
09	497.0	38.0	25.0	9371.0
10	20.0	51.0	2.0	9858.0
11	9920.0	2.0	2.0	7.0
12	6054.0	3.0	6.0	3868.0
13	10.0	9909.0	3.0	9.0
14	2.0	9912.0	2.0	15.0
15	99.0	10.0	9811.0	11.0
16	75.0	22.0	9723.0	111.0
17	9630.0	173.0	29.0	99.0
18	9333.25	198.25	158.25	241.25
19	1928.75	2777.75	661.75	4562.75

PFM

	A	C	G	T
01	0.38	0.271	0.179	0.17
02	0.461	0.233	0.275	0.031
03	0.029	0.948	0.009	0.015
04	0.003	0.924	0.001	0.072
05	0.001	0.139	0.001	0.859
06	0.001	0.996	0.001	0.002
07	0.479	0.007	0.509	0.005
08	0.348	0.176	0.366	0.11
09	0.05	0.004	0.003	0.944
10	0.002	0.005	0.0	0.993
11	0.999	0.0	0.0	0.001
12	0.61	0.0	0.001	0.389
13	0.001	0.998	0.0	0.001
14	0.0	0.998	0.0	0.002
15	0.01	0.001	0.988	0.001
16	0.008	0.002	0.979	0.011
17	0.97	0.017	0.003	0.01
18	0.94	0.02	0.016	0.024
19	0.194	0.28	0.067	0.459

PWM

	A	C	G	T
01	0.418	0.08	-0.335	-0.383
02	0.612	-0.07	0.094	-2.089
03	-2.151	1.332	-3.349	-2.805
04	-4.312	1.306	-5.393	-1.24
05	-5.23	-0.584	-5.393	1.233
06	-5.09	1.382	-5.588	-4.911
07	0.651	-3.537	0.71	-3.9
08	0.332	-0.353	0.381	-0.82
09	-1.605	-4.122	-4.511	1.328
10	-4.713	-3.842	-6.359	1.378
11	1.384	-6.359	-6.359	-5.588
12	0.891	-6.15	-5.702	0.443
13	-5.308	1.383	-6.15	-5.393
14	-6.359	1.384	-6.359	-4.967
15	-3.2	-5.308	1.373	-5.23
16	-3.47	-4.628	1.364	-3.088
17	1.355	-2.652	-4.374	-3.2
18	1.324	-2.517	-2.739	-2.323
19	-0.252	0.112	-1.32	0.608

Standard thresholds

P-value	Threshold
0.001	-8.32839
0.0005	-6.15599
0.0001	-1.54884