RFX1.H12RSNP.2.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX1.H12RSNP.2.S.C
Gene (human)	RFX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	10
Consensus	nSGTTGCYnn
GC content	54.75%
Information content (bits; total / per base)	11.141 / 1.114
Data sources	HT-SELEX
Aligned words	1887

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)	0.835	0.862	0.752	0.784	0.752	0.78	2.183	2.349	360.658	480.357
Mouse	4 (20)	0.822	0.844	0.704	0.728	0.738	0.769	2.111	2.22	353.87	415.721

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.951	0.932	0.874	0.858	0.758	0.759
Overall, 4 experiments	best	0.98	0.973	0.971	0.953	0.904	0.892
Methyl HT-SELEX, 2 experiments	median	0.89	0.85	0.835	0.804	0.735	0.726
Methyl HT-SELEX, 2 experiments	best	0.955	0.936	0.95	0.921	0.843	0.831
Non-Methyl HT-SELEX, 2 experiments	median	0.963	0.95	0.885	0.874	0.789	0.789
Non-Methyl HT-SELEX, 2 experiments	best	0.98	0.973	0.971	0.953	0.904	0.892

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.5	6.947	0.127	0.05

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.634	0.188	0.58	0.419
batch 2	0.612	0.376	0.765	0.547

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.H12RSNP.2.S.C.pcm
PWM	RFX1.H12RSNP.2.S.C.pwm
PFM	RFX1.H12RSNP.2.S.C.pfm
Alignment	RFX1.H12RSNP.2.S.C.words.tsv
Threshold to P-value map	RFX1.H12RSNP.2.S.C.thr
Motif in other formats
JASPAR format	RFX1.H12RSNP.2.S.C_jaspar_format.txt
MEME format	RFX1.H12RSNP.2.S.C_meme_format.meme
Transfac format	RFX1.H12RSNP.2.S.C_transfac_format.txt
Homer format	RFX1.H12RSNP.2.S.C_homer_format_0.001.txt RFX1.H12RSNP.2.S.C_homer_format_0.0005.txt RFX1.H12RSNP.2.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	445.75	343.75	581.75	515.75
02	68.0	735.0	917.0	167.0
03	0.0	0.0	1887.0	0.0
04	0.0	0.0	1.0	1886.0
05	3.0	0.0	0.0	1884.0
06	0.0	0.0	1887.0	0.0
07	0.0	1813.0	74.0	0.0
08	27.0	320.0	193.0	1347.0
09	737.0	330.0	360.0	460.0
10	409.5	376.5	511.5	589.5

PFM

	A	C	G	T
01	0.236	0.182	0.308	0.273
02	0.036	0.39	0.486	0.089
03	0.0	0.0	1.0	0.0
04	0.0	0.0	0.001	0.999
05	0.002	0.0	0.0	0.998
06	0.0	0.0	1.0	0.0
07	0.0	0.961	0.039	0.0
08	0.014	0.17	0.102	0.714
09	0.391	0.175	0.191	0.244
10	0.217	0.2	0.271	0.312

PWM

	A	C	G	T
01	-0.056	-0.315	0.209	0.089
02	-1.914	0.442	0.663	-1.031
03	-5.526	-5.526	1.383	-5.526
04	-5.526	-5.526	-5.101	1.383
05	-4.574	-5.526	-5.526	1.382
06	-5.526	-5.526	1.383	-5.526
07	-5.526	1.343	-1.831	-5.526
08	-2.797	-0.386	-0.888	1.047
09	0.445	-0.356	-0.269	-0.025
10	-0.141	-0.225	0.081	0.222

Standard thresholds

P-value	Threshold
0.001	3.9512
0.0005	5.68794
0.0001	8.01179