RFX5.H13RSNP.0.PSG.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX5.H13RSNP.0.PSG.D
Gene (human)	RFX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	19
Consensus	vbbGTTGCCAKGGvRAYvS
GC content	59.23%
Information content (bits; total / per base)	18.573 / 0.978
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX
Aligned words	425
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	2 (2)	0.917	0.921	0.9	0.904	0.644	0.656	152.649	172.137

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
GFPIVT, 1 experiments	median	1.0	1.0	0.953	0.951	0.84	0.841
GFPIVT, 1 experiments	best	1.0	1.0	0.953	0.951	0.84	0.841

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
GFPIVT, 1 experiments	median	202.424	0.632	0.712	0.701
GFPIVT, 1 experiments	best	218.538	0.657	0.74	0.722

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Fork head/winged helix factors {3.3} (TFClass)
TF family	RFX {3.3.3} (TFClass)
TF subfamily	{3.3.3.0} (TFClass)
TFClass ID	TFClass: 3.3.3.0.5
HGNC	HGNC:9986
MGI	MGI:1858421
EntrezGene (human)	GeneID:5993 (SSTAR profile)
EntrezGene (mouse)	GeneID:53970 (SSTAR profile)
UniProt ID (human)	RFX5_HUMAN
UniProt ID (mouse)	RFX5_MOUSE
UniProt AC (human)	P48382 (TFClass)
UniProt AC (mouse)	Q9JL61 (TFClass)
GRECO-DB-TF	yes

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

PCM	RFX5.H13RSNP.0.PSG.D.pcm
PWM	RFX5.H13RSNP.0.PSG.D.pwm
PFM	RFX5.H13RSNP.0.PSG.D.pfm
Threshold to P-value map	RFX5.H13RSNP.0.PSG.D.thr
Motif in other formats
JASPAR format	RFX5.H13RSNP.0.PSG.D_jaspar_format.txt
MEME format	RFX5.H13RSNP.0.PSG.D_meme_format.meme
Transfac format	RFX5.H13RSNP.0.PSG.D_transfac_format.txt
Homer format	RFX5.H13RSNP.0.PSG.D_homer_format_0.001.txt RFX5.H13RSNP.0.PSG.D_homer_format_0.0005.txt RFX5.H13RSNP.0.PSG.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	52.0	106.0	227.0	40.0
02	37.0	132.0	173.0	83.0
03	27.0	84.0	158.0	156.0
04	0.0	0.0	425.0	0.0
05	0.0	4.0	4.0	417.0
06	3.0	26.0	1.0	395.0
07	23.0	2.0	375.0	25.0
08	1.0	384.0	4.0	36.0
09	1.0	341.0	1.0	82.0
10	359.0	13.0	29.0	24.0
11	31.0	17.0	56.0	321.0
12	20.0	2.0	401.0	2.0
13	41.0	18.0	365.0	1.0
14	80.0	225.0	61.0	59.0
15	247.0	13.0	131.0	34.0
16	372.0	15.0	19.0	19.0
17	30.0	296.0	18.0	81.0
18	87.0	110.0	181.0	47.0
19	30.0	128.0	238.0	29.0

PFM

	A	C	G	T
01	0.122	0.249	0.534	0.094
02	0.087	0.311	0.407	0.195
03	0.064	0.198	0.372	0.367
04	0.0	0.0	1.0	0.0
05	0.0	0.009	0.009	0.981
06	0.007	0.061	0.002	0.929
07	0.054	0.005	0.882	0.059
08	0.002	0.904	0.009	0.085
09	0.002	0.802	0.002	0.193
10	0.845	0.031	0.068	0.056
11	0.073	0.04	0.132	0.755
12	0.047	0.005	0.944	0.005
13	0.096	0.042	0.859	0.002
14	0.188	0.529	0.144	0.139
15	0.581	0.031	0.308	0.08
16	0.875	0.035	0.045	0.045
17	0.071	0.696	0.042	0.191
18	0.205	0.259	0.426	0.111
19	0.071	0.301	0.56	0.068

PWM

	A	C	G	T
01	-0.7	-0.002	0.752	-0.954
02	-1.029	0.214	0.482	-0.243
03	-1.33	-0.231	0.392	0.38
04	-4.266	-4.266	1.376	-4.266
05	-4.266	-2.973	-2.973	1.357
06	-3.173	-1.365	-3.758	1.303
07	-1.481	-3.423	1.251	-1.402
08	-3.758	1.275	-2.973	-1.055
09	-3.758	1.156	-3.758	-0.255
10	1.208	-2.005	-1.262	-1.441
11	-1.198	-1.761	-0.628	1.096
12	-1.611	-3.423	1.318	-3.423
13	-0.93	-1.709	1.224	-3.758
14	-0.279	0.743	-0.545	-0.577
15	0.836	-2.005	0.207	-1.11
16	1.243	-1.876	-1.659	-1.659
17	-1.23	1.016	-1.709	-0.267
18	-0.197	0.034	0.527	-0.798
19	-1.23	0.184	0.799	-1.262

Standard thresholds

P-value	Threshold
0.001	1.60781
0.0005	2.90381
0.0001	5.63246