RFX2.H12RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX2.H12RSNP.0.PS.A
Gene (human)	RFX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	bbGTTKCYWKGR
GC content	53.18%
Information content (bits; total / per base)	11.124 / 0.927
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1160

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	2 (13)	0.844	0.947	0.803	0.9	0.866	0.934	4.171	4.321	64.31	485.004
Mouse	2 (14)	0.968	0.978	0.938	0.96	0.962	0.978	5.425	5.98	387.704	602.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.994	0.991	0.873	0.879	0.701	0.735
Overall, 6 experiments	best	1.0	1.0	0.999	0.999	0.999	0.998
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.998	0.997	0.947	0.949
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.998	0.997	0.947	0.949
Non-Methyl HT-SELEX, 5 experiments	median	0.993	0.991	0.859	0.869	0.689	0.726
Non-Methyl HT-SELEX, 5 experiments	best	1.0	1.0	0.999	0.999	0.999	0.998

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.905	0.484	0.878	0.531

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: 3.3.3.0.2
HGNC	HGNC:9983
MGI	MGI:106583
EntrezGene (human)	GeneID:5990 (SSTAR profile)
EntrezGene (mouse)	GeneID:19725 (SSTAR profile)
UniProt ID (human)	RFX2_HUMAN
UniProt ID (mouse)	RFX2_MOUSE
UniProt AC (human)	P48378 (TFClass)
UniProt AC (mouse)	P48379 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 2 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	RFX2.H12RSNP.0.PS.A.pcm
PWM	RFX2.H12RSNP.0.PS.A.pwm
PFM	RFX2.H12RSNP.0.PS.A.pfm
Alignment	RFX2.H12RSNP.0.PS.A.words.tsv
Threshold to P-value map	RFX2.H12RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	RFX2.H12RSNP.0.PS.A_jaspar_format.txt
MEME format	RFX2.H12RSNP.0.PS.A_meme_format.meme
Transfac format	RFX2.H12RSNP.0.PS.A_transfac_format.txt
Homer format	RFX2.H12RSNP.0.PS.A_homer_format_0.001.txt RFX2.H12RSNP.0.PS.A_homer_format_0.0005.txt RFX2.H12RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	105.0	545.0	167.0	343.0
02	171.0	192.0	377.0	420.0
03	17.0	34.0	1025.0	84.0
04	11.0	35.0	11.0	1103.0
05	17.0	50.0	33.0	1060.0
06	59.0	31.0	866.0	204.0
07	32.0	982.0	14.0	132.0
08	34.0	750.0	10.0	366.0
09	886.0	64.0	52.0	158.0
10	201.0	36.0	211.0	712.0
11	100.0	10.0	974.0	76.0
12	159.0	74.0	860.0	67.0

PFM

	A	C	G	T
01	0.091	0.47	0.144	0.296
02	0.147	0.166	0.325	0.362
03	0.015	0.029	0.884	0.072
04	0.009	0.03	0.009	0.951
05	0.015	0.043	0.028	0.914
06	0.051	0.027	0.747	0.176
07	0.028	0.847	0.012	0.114
08	0.029	0.647	0.009	0.316
09	0.764	0.055	0.045	0.136
10	0.173	0.031	0.182	0.614
11	0.086	0.009	0.84	0.066
12	0.137	0.064	0.741	0.058

PWM

	A	C	G	T
01	-1.005	0.628	-0.547	0.167
02	-0.524	-0.409	0.261	0.369
03	-2.744	-2.099	1.258	-1.224
04	-3.129	-2.071	-3.129	1.331
05	-2.744	-1.729	-2.127	1.292
06	-1.569	-2.187	1.09	-0.349
07	-2.157	1.215	-2.918	-0.78
08	-2.099	0.946	-3.211	0.231
09	1.113	-1.49	-1.691	-0.602
10	-0.364	-2.045	-0.316	0.895
11	-1.053	-3.211	1.207	-1.322
12	-0.596	-1.348	1.083	-1.445

Standard thresholds

P-value	Threshold
0.001	4.442775
0.0005	5.331825
0.0001	7.182935