RFX1.H13RSNP.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX1.H13RSNP.0.PM.A
Gene (human)	RFX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	dGTTRCCAKGR
GC content	53.09%
Information content (bits; total / per base)	11.641 / 1.058
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	1010
Previous names	RFX1.H12RSNP.0.PM.A

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	5 (35)	0.951	0.984	0.922	0.972	0.941	0.981	4.768	6.013	638.26	893.569
Mouse	4 (20)	0.95	0.959	0.912	0.93	0.94	0.949	4.694	5.304	648.004	793.222

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.989	0.985	0.954	0.946	0.876	0.879
Overall, 4 experiments	best	1.0	1.0	0.999	0.999	0.993	0.992
Methyl HT-SELEX, 2 experiments	median	0.989	0.985	0.954	0.946	0.876	0.879
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.999	0.998	0.986	0.984
Non-Methyl HT-SELEX, 2 experiments	median	0.986	0.973	0.939	0.931	0.856	0.864
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.999	0.999	0.993	0.992

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.37	11.642	0.174	0.095

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.954	0.63	0.924	0.566
batch 2	0.937	0.832	0.862	0.48

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: 3.3.3.0.1
HGNC	HGNC:9982
MGI	MGI:105982
EntrezGene (human)	GeneID:5989 (SSTAR profile)
EntrezGene (mouse)	GeneID:19724 (SSTAR profile)
UniProt ID (human)	RFX1_HUMAN
UniProt ID (mouse)	RFX1_MOUSE
UniProt AC (human)	P22670 (TFClass)
UniProt AC (mouse)	P48377 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 4 mouse
HT-SELEX	2
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	RFX1.H13RSNP.0.PM.A.pcm
PWM	RFX1.H13RSNP.0.PM.A.pwm
PFM	RFX1.H13RSNP.0.PM.A.pfm
Threshold to P-value map	RFX1.H13RSNP.0.PM.A.thr
Motif in other formats
JASPAR format	RFX1.H13RSNP.0.PM.A_jaspar_format.txt
MEME format	RFX1.H13RSNP.0.PM.A_meme_format.meme
Transfac format	RFX1.H13RSNP.0.PM.A_transfac_format.txt
Homer format	RFX1.H13RSNP.0.PM.A_homer_format_0.001.txt RFX1.H13RSNP.0.PM.A_homer_format_0.0005.txt RFX1.H13RSNP.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	170.0	116.0	324.0	400.0
02	54.0	4.0	943.0	9.0
03	12.0	35.0	9.0	954.0
04	51.0	63.0	18.0	878.0
05	148.0	25.0	731.0	106.0
06	1.0	871.0	13.0	125.0
07	9.0	707.0	10.0	284.0
08	819.0	53.0	52.0	86.0
09	147.0	36.0	148.0	679.0
10	95.0	12.0	884.0	19.0
11	135.0	62.0	782.0	31.0

PFM

	A	C	G	T
01	0.168	0.115	0.321	0.396
02	0.053	0.004	0.934	0.009
03	0.012	0.035	0.009	0.945
04	0.05	0.062	0.018	0.869
05	0.147	0.025	0.724	0.105
06	0.001	0.862	0.013	0.124
07	0.009	0.7	0.01	0.281
08	0.811	0.052	0.051	0.085
09	0.146	0.036	0.147	0.672
10	0.094	0.012	0.875	0.019
11	0.134	0.061	0.774	0.031

PWM

	A	C	G	T
01	-0.392	-0.77	0.248	0.458
02	-1.518	-3.793	1.313	-3.165
03	-2.919	-1.935	-3.165	1.324
04	-1.573	-1.368	-2.556	1.241
05	-0.529	-2.252	1.059	-0.859
06	-4.534	1.233	-2.848	-0.696
07	-3.165	1.025	-3.076	0.117
08	1.172	-1.536	-1.554	-1.064
09	-0.536	-1.908	-0.529	0.985
10	-0.966	-2.919	1.248	-2.507
11	-0.62	-1.384	1.126	-2.05

Standard thresholds

P-value	Threshold
0.001	4.304985
0.0005	5.244465
0.0001	7.163935