RFX5.H13INVITRO.0.PSG.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX5.H13INVITRO.0.PSG.A
Gene (human)	RFX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	21
Consensus	dbKGTTGCSATGGYAACvRdn
GC content	54.34%
Information content (bits; total / per base)	22.131 / 1.054
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX
Aligned words	306
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)	0.827	0.832	0.829	0.833	0.638	0.651	120.051	141.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
GFPIVT, 1 experiments	median	1.0	1.0	0.898	0.903	0.741	0.763
GFPIVT, 1 experiments	best	1.0	1.0	0.898	0.903	0.741	0.763

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
GFPIVT, 1 experiments	median	192.111	0.724	0.738	0.72
GFPIVT, 1 experiments	best	206.301	0.745	0.75	0.735

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.H13INVITRO.0.PSG.A.pcm
PWM	RFX5.H13INVITRO.0.PSG.A.pwm
PFM	RFX5.H13INVITRO.0.PSG.A.pfm
Threshold to P-value map	RFX5.H13INVITRO.0.PSG.A.thr
Motif in other formats
JASPAR format	RFX5.H13INVITRO.0.PSG.A_jaspar_format.txt
MEME format	RFX5.H13INVITRO.0.PSG.A_meme_format.meme
Transfac format	RFX5.H13INVITRO.0.PSG.A_transfac_format.txt
Homer format	RFX5.H13INVITRO.0.PSG.A_homer_format_0.001.txt RFX5.H13INVITRO.0.PSG.A_homer_format_0.0005.txt RFX5.H13INVITRO.0.PSG.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	41.0	38.0	175.0	52.0
02	38.0	61.0	91.0	116.0
03	22.0	18.0	169.0	97.0
04	1.0	0.0	305.0	0.0
05	1.0	0.0	0.0	305.0
06	0.0	3.0	59.0	244.0
07	38.0	0.0	258.0	10.0
08	1.0	247.0	0.0	58.0
09	1.0	205.0	56.0	44.0
10	274.0	1.0	30.0	1.0
11	2.0	1.0	5.0	298.0
12	18.0	0.0	288.0	0.0
13	1.0	0.0	305.0	0.0
14	19.0	154.0	7.0	126.0
15	249.0	0.0	56.0	1.0
16	291.0	0.0	15.0	0.0
17	1.0	247.0	4.0	54.0
18	96.0	51.0	115.0	44.0
19	40.0	37.0	206.0	23.0
20	58.0	34.0	74.0	140.0
21	88.0	41.0	136.0	41.0

PFM

	A	C	G	T
01	0.134	0.124	0.572	0.17
02	0.124	0.199	0.297	0.379
03	0.072	0.059	0.552	0.317
04	0.003	0.0	0.997	0.0
05	0.003	0.0	0.0	0.997
06	0.0	0.01	0.193	0.797
07	0.124	0.0	0.843	0.033
08	0.003	0.807	0.0	0.19
09	0.003	0.67	0.183	0.144
10	0.895	0.003	0.098	0.003
11	0.007	0.003	0.016	0.974
12	0.059	0.0	0.941	0.0
13	0.003	0.0	0.997	0.0
14	0.062	0.503	0.023	0.412
15	0.814	0.0	0.183	0.003
16	0.951	0.0	0.049	0.0
17	0.003	0.807	0.013	0.176
18	0.314	0.167	0.376	0.144
19	0.131	0.121	0.673	0.075
20	0.19	0.111	0.242	0.458
21	0.288	0.134	0.444	0.134

PWM

	A	C	G	T
01	-0.608	-0.681	0.817	-0.377
02	-0.681	-0.222	0.171	0.41
03	-1.202	-1.389	0.783	0.234
04	-3.468	-3.998	1.369	-3.998
05	-3.468	-3.998	-3.998	1.369
06	-3.998	-2.867	-0.254	1.147
07	-0.681	-3.998	1.203	-1.92
08	-3.468	1.159	-3.998	-0.271
09	-3.468	0.974	-0.305	-0.54
10	1.263	-3.468	-0.908	-3.468
11	-3.123	-3.468	-2.495	1.346
12	-1.389	-3.998	1.312	-3.998
13	-3.468	-3.998	1.369	-3.998
14	-1.339	0.69	-2.224	0.492
15	1.167	-3.998	-0.305	-3.468
16	1.322	-3.998	-1.557	-3.998
17	-3.468	1.159	-2.664	-0.341
18	0.223	-0.396	0.401	-0.54
19	-0.632	-0.707	0.979	-1.16
20	-0.271	-0.788	-0.033	0.596
21	0.138	-0.608	0.567	-0.608

Standard thresholds

P-value	Threshold
0.001	-0.84359
0.0005	0.70246
0.0001	3.97456