RFX5.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX5.H12INVIVO.0.P.B
Gene (human)	RFX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	20
Consensus	vbvvbYdGTYRCYRKGbvvv
GC content	55.55%
Information content (bits; total / per base)	12.313 / 0.616
Data sources	ChIP-Seq
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	6 (41)	0.882	0.964	0.844	0.94	0.873	0.954	4.336	5.593	289.292	548.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.983	0.973	0.921	0.912	0.815	0.823
Overall, 4 experiments	best	0.993	0.988	0.988	0.98	0.974	0.963
Methyl HT-SELEX, 1 experiments	median	0.985	0.975	0.973	0.958	0.939	0.919
Methyl HT-SELEX, 1 experiments	best	0.985	0.975	0.973	0.958	0.939	0.919
Non-Methyl HT-SELEX, 3 experiments	median	0.981	0.971	0.869	0.867	0.692	0.726
Non-Methyl HT-SELEX, 3 experiments	best	0.993	0.988	0.988	0.98	0.974	0.963

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.066	0.954	0.094	-0.006

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.659	0.259	0.617	0.423

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	6 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	RFX5.H12INVIVO.0.P.B.pcm
PWM	RFX5.H12INVIVO.0.P.B.pwm
PFM	RFX5.H12INVIVO.0.P.B.pfm
Alignment	RFX5.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	RFX5.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	RFX5.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	RFX5.H12INVIVO.0.P.B_meme_format.meme
Transfac format	RFX5.H12INVIVO.0.P.B_transfac_format.txt
Homer format	RFX5.H12INVIVO.0.P.B_homer_format_0.001.txt RFX5.H12INVIVO.0.P.B_homer_format_0.0005.txt RFX5.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	194.0	202.0	500.0	104.0
02	99.0	175.0	192.0	534.0
03	151.0	579.0	155.0	115.0
04	533.0	180.0	179.0	108.0
05	97.0	296.0	324.0	283.0
06	48.0	606.0	125.0	221.0
07	263.0	71.0	191.0	475.0
08	24.0	13.0	960.0	3.0
09	7.0	38.0	28.0	927.0
10	74.0	168.0	19.0	739.0
11	184.0	18.0	661.0	137.0
12	15.0	901.0	26.0	58.0
13	9.0	455.0	23.0	513.0
14	679.0	20.0	264.0	37.0
15	155.0	44.0	611.0	190.0
16	45.0	67.0	852.0	36.0
17	136.0	393.0	319.0	152.0
18	450.0	190.0	252.0	108.0
19	315.0	119.0	495.0	71.0
20	476.0	166.0	233.0	125.0

PFM

	A	C	G	T
01	0.194	0.202	0.5	0.104
02	0.099	0.175	0.192	0.534
03	0.151	0.579	0.155	0.115
04	0.533	0.18	0.179	0.108
05	0.097	0.296	0.324	0.283
06	0.048	0.606	0.125	0.221
07	0.263	0.071	0.191	0.475
08	0.024	0.013	0.96	0.003
09	0.007	0.038	0.028	0.927
10	0.074	0.168	0.019	0.739
11	0.184	0.018	0.661	0.137
12	0.015	0.901	0.026	0.058
13	0.009	0.455	0.023	0.513
14	0.679	0.02	0.264	0.037
15	0.155	0.044	0.611	0.19
16	0.045	0.067	0.852	0.036
17	0.136	0.393	0.319	0.152
18	0.45	0.19	0.252	0.108
19	0.315	0.119	0.495	0.071
20	0.476	0.166	0.233	0.125

PWM

	A	C	G	T
01	-0.252	-0.212	0.69	-0.867
02	-0.916	-0.354	-0.262	0.755
03	-0.5	0.836	-0.474	-0.769
04	0.753	-0.326	-0.331	-0.83
05	-0.936	0.168	0.258	0.123
06	-1.622	0.881	-0.686	-0.122
07	0.05	-1.242	-0.267	0.639
08	-2.281	-2.839	1.34	-3.975
09	-3.362	-1.846	-2.136	1.305
10	-1.201	-0.394	-2.497	1.079
11	-0.304	-2.546	0.968	-0.596
12	-2.711	1.277	-2.206	-1.439
13	-3.156	0.596	-2.32	0.715
14	0.995	-2.45	0.054	-1.872
15	-0.474	-1.706	0.89	-0.272
16	-1.684	-1.298	1.221	-1.898
17	-0.603	0.45	0.242	-0.493
18	0.585	-0.272	0.008	-0.83
19	0.23	-0.735	0.68	-1.242
20	0.641	-0.406	-0.07	-0.686

Standard thresholds

P-value	Threshold
0.001	4.16656
0.0005	5.10126
0.0001	7.05136