RFX1.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX1.H12INVIVO.1.PSM.A
Gene (human)	RFX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	16
Consensus	YbGTTGCCAWGGnRMC
GC content	56.36%
Information content (bits; total / per base)	16.935 / 1.058
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	762

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)	0.976	0.992	0.955	0.984	0.968	0.989	6.521	8.288	698.796	939.046
Mouse	4 (20)	0.968	0.976	0.945	0.959	0.958	0.966	6.528	7.653	705.604	854.284

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.995	0.994	0.957	0.954	0.871	0.881
Overall, 4 experiments	best	1.0	1.0	1.0	1.0	0.994	0.994
Methyl HT-SELEX, 2 experiments	median	0.995	0.994	0.957	0.954	0.871	0.881
Methyl HT-SELEX, 2 experiments	best	1.0	1.0	1.0	1.0	0.989	0.989
Non-Methyl HT-SELEX, 2 experiments	median	0.856	0.856	0.794	0.804	0.762	0.775
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	1.0	1.0	0.994	0.994

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.38	11.505	0.201	0.103

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.926	0.48	0.901	0.547
batch 2	0.924	0.783	0.809	0.427

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

PCM	RFX1.H12INVIVO.1.PSM.A.pcm
PWM	RFX1.H12INVIVO.1.PSM.A.pwm
PFM	RFX1.H12INVIVO.1.PSM.A.pfm
Alignment	RFX1.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	RFX1.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	RFX1.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	RFX1.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	RFX1.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	RFX1.H12INVIVO.1.PSM.A_homer_format_0.001.txt RFX1.H12INVIVO.1.PSM.A_homer_format_0.0005.txt RFX1.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	30.0	438.0	114.0	180.0
02	96.0	160.0	257.0	249.0
03	1.0	0.0	761.0	0.0
04	1.0	23.0	2.0	736.0
05	20.0	56.0	4.0	682.0
06	37.0	1.0	674.0	50.0
07	3.0	705.0	1.0	53.0
08	0.0	561.0	0.0	201.0
09	619.0	32.0	40.0	71.0
10	130.0	20.0	122.0	490.0
11	36.0	1.0	724.0	1.0
12	81.0	21.0	646.0	14.0
13	176.0	299.0	151.0	136.0
14	428.0	31.0	248.0	55.0
15	601.0	91.0	53.0	17.0
16	42.0	612.0	24.0	84.0

PFM

	A	C	G	T
01	0.039	0.575	0.15	0.236
02	0.126	0.21	0.337	0.327
03	0.001	0.0	0.999	0.0
04	0.001	0.03	0.003	0.966
05	0.026	0.073	0.005	0.895
06	0.049	0.001	0.885	0.066
07	0.004	0.925	0.001	0.07
08	0.0	0.736	0.0	0.264
09	0.812	0.042	0.052	0.093
10	0.171	0.026	0.16	0.643
11	0.047	0.001	0.95	0.001
12	0.106	0.028	0.848	0.018
13	0.231	0.392	0.198	0.178
14	0.562	0.041	0.325	0.072
15	0.789	0.119	0.07	0.022
16	0.055	0.803	0.031	0.11

PWM

	A	C	G	T
01	-1.803	0.828	-0.508	-0.056
02	-0.677	-0.173	0.297	0.266
03	-4.28	-4.752	1.378	-4.752
04	-4.28	-2.053	-3.961	1.345
05	-2.183	-1.204	-3.525	1.269
06	-1.604	-4.28	1.257	-1.314
07	-3.72	1.302	-4.28	-1.257
08	-4.752	1.074	-4.752	0.053
09	1.172	-1.742	-1.529	-0.973
10	-0.378	-2.183	-0.441	0.939
11	-1.63	-4.28	1.329	-4.28
12	-0.844	-2.138	1.215	-2.507
13	-0.078	0.448	-0.23	-0.334
14	0.805	-1.772	0.262	-1.221
15	1.143	-0.729	-1.257	-2.332
16	-1.482	1.161	-2.013	-0.808

Standard thresholds

P-value	Threshold
0.001	2.05701
0.0005	3.34991
0.0001	6.03931