RFX3.H12RSNP.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX3.H12RSNP.1.PS.A
Gene (human)	RFX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx3
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	17
Consensus	nnbSGTTGCCATGGYWM
GC content	53.84%
Information content (bits; total / per base)	21.142 / 1.244
Data sources	ChIP-Seq + HT-SELEX
Aligned words	327

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	1 (7)	0.822	0.833	0.807	0.819	0.904	0.909	4.802	4.963	610.444	621.721
Mouse	1 (5)	0.822	0.826	0.808	0.811	0.916	0.917	5.083	5.102	628.26	702.357

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.711	0.73	0.592	0.616	0.542	0.564
Overall, 6 experiments	best	1.0	1.0	1.0	1.0	0.932	0.94
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	1.0	0.932	0.94
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	0.932	0.94
Non-Methyl HT-SELEX, 5 experiments	median	0.643	0.673	0.558	0.58	0.526	0.542
Non-Methyl HT-SELEX, 5 experiments	best	1.0	1.0	1.0	1.0	0.895	0.909

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.76	0.516	0.834	0.647

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: 3.3.3.0.3
HGNC	HGNC:9984
MGI	MGI:106582
EntrezGene (human)	GeneID:5991 (SSTAR profile)
EntrezGene (mouse)	GeneID:19726 (SSTAR profile)
UniProt ID (human)	RFX3_HUMAN
UniProt ID (mouse)	RFX3_MOUSE
UniProt AC (human)	P48380 (TFClass)
UniProt AC (mouse)	P48381 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 1 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	RFX3.H12RSNP.1.PS.A.pcm
PWM	RFX3.H12RSNP.1.PS.A.pwm
PFM	RFX3.H12RSNP.1.PS.A.pfm
Alignment	RFX3.H12RSNP.1.PS.A.words.tsv
Threshold to P-value map	RFX3.H12RSNP.1.PS.A.thr
Motif in other formats
JASPAR format	RFX3.H12RSNP.1.PS.A_jaspar_format.txt
MEME format	RFX3.H12RSNP.1.PS.A_meme_format.meme
Transfac format	RFX3.H12RSNP.1.PS.A_transfac_format.txt
Homer format	RFX3.H12RSNP.1.PS.A_homer_format_0.001.txt RFX3.H12RSNP.1.PS.A_homer_format_0.0005.txt RFX3.H12RSNP.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	102.75	66.75	108.75	48.75
02	104.25	75.25	99.25	48.25
03	36.0	153.0	57.0	81.0
04	16.0	171.0	118.0	22.0
05	0.0	0.0	327.0	0.0
06	0.0	0.0	0.0	327.0
07	5.0	1.0	0.0	321.0
08	24.0	0.0	302.0	1.0
09	0.0	326.0	0.0	1.0
10	0.0	296.0	0.0	31.0
11	327.0	0.0	0.0	0.0
12	0.0	0.0	1.0	326.0
13	6.0	0.0	321.0	0.0
14	15.0	1.0	310.0	1.0
15	17.0	154.0	10.0	146.0
16	168.25	19.25	16.25	123.25
17	237.75	30.75	28.75	29.75

PFM

	A	C	G	T
01	0.314	0.204	0.333	0.149
02	0.319	0.23	0.304	0.148
03	0.11	0.468	0.174	0.248
04	0.049	0.523	0.361	0.067
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.0	1.0
07	0.015	0.003	0.0	0.982
08	0.073	0.0	0.924	0.003
09	0.0	0.997	0.0	0.003
10	0.0	0.905	0.0	0.095
11	1.0	0.0	0.0	0.0
12	0.0	0.0	0.003	0.997
13	0.018	0.0	0.982	0.0
14	0.046	0.003	0.948	0.003
15	0.052	0.471	0.031	0.446
16	0.515	0.059	0.05	0.377
17	0.727	0.094	0.088	0.091

PWM

	A	C	G	T
01	0.225	-0.199	0.281	-0.505
02	0.239	-0.081	0.191	-0.515
03	-0.798	0.619	-0.353	-0.009
04	-1.562	0.729	0.362	-1.266
05	-4.051	-4.051	1.373	-4.051
06	-4.051	-4.051	-4.051	1.373
07	-2.558	-3.526	-4.051	1.355
08	-1.185	-4.051	1.294	-3.526
09	-4.051	1.37	-4.051	-3.526
10	-4.051	1.274	-4.051	-0.942
11	1.373	-4.051	-4.051	-4.051
12	-4.051	-4.051	-3.526	1.37
13	-2.413	-4.051	1.355	-4.051
14	-1.621	-3.526	1.32	-3.526
15	-1.506	0.625	-1.983	0.572
16	0.713	-1.391	-1.548	0.405
17	1.056	-0.949	-1.013	-0.981

Standard thresholds

P-value	Threshold
0.001	-0.98939
0.0005	0.62871
0.0001	3.97381