RFX2.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX2.H12RSNP.1.PSM.A
Gene (human)	RFX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	20
Consensus	nhhCGTTGCCATGGCAACRn
GC content	57.69%
Information content (bits; total / per base)	29.493 / 1.475
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	607

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)	0.511	0.528	0.368	0.408	0.808	0.878	4.748	5.158	63.602	368.42
Mouse	2 (14)	0.528	0.544	0.406	0.441	0.918	0.947	6.345	7.164	316.502	539.377

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.997	0.996	0.846	0.859	0.682	0.719
Overall, 6 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	1.0	0.946	0.951
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	0.946	0.951
Non-Methyl HT-SELEX, 5 experiments	median	0.995	0.994	0.843	0.859	0.674	0.716
Non-Methyl HT-SELEX, 5 experiments	best	1.0	1.0	1.0	1.0	1.0	1.0

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.921	0.505	0.9	0.584

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.1.PSM.A.pcm
PWM	RFX2.H12RSNP.1.PSM.A.pwm
PFM	RFX2.H12RSNP.1.PSM.A.pfm
Alignment	RFX2.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	RFX2.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	RFX2.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	RFX2.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	RFX2.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	RFX2.H12RSNP.1.PSM.A_homer_format_0.001.txt RFX2.H12RSNP.1.PSM.A_homer_format_0.0005.txt RFX2.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	164.5	153.5	127.5	161.5
02	262.5	141.5	91.5	111.5
03	73.0	264.0	37.0	233.0
04	0.0	312.0	295.0	0.0
05	0.0	0.0	607.0	0.0
06	0.0	0.0	0.0	607.0
07	1.0	0.0	0.0	606.0
08	102.0	0.0	503.0	2.0
09	0.0	607.0	0.0	0.0
10	0.0	607.0	0.0	0.0
11	607.0	0.0	0.0	0.0
12	0.0	0.0	0.0	607.0
13	0.0	0.0	607.0	0.0
14	0.0	0.0	607.0	0.0
15	0.0	575.0	0.0	32.0
16	607.0	0.0	0.0	0.0
17	607.0	0.0	0.0	0.0
18	0.0	607.0	0.0	0.0
19	68.0	12.0	481.0	46.0
20	135.5	176.5	191.5	103.5

PFM

	A	C	G	T
01	0.271	0.253	0.21	0.266
02	0.432	0.233	0.151	0.184
03	0.12	0.435	0.061	0.384
04	0.0	0.514	0.486	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.0	1.0
07	0.002	0.0	0.0	0.998
08	0.168	0.0	0.829	0.003
09	0.0	1.0	0.0	0.0
10	0.0	1.0	0.0	0.0
11	1.0	0.0	0.0	0.0
12	0.0	0.0	0.0	1.0
13	0.0	0.0	1.0	0.0
14	0.0	0.0	1.0	0.0
15	0.0	0.947	0.0	0.053
16	1.0	0.0	0.0	0.0
17	1.0	0.0	0.0	0.0
18	0.0	1.0	0.0	0.0
19	0.112	0.02	0.792	0.076
20	0.223	0.291	0.315	0.171

PWM

	A	C	G	T
01	0.08	0.011	-0.172	0.062
02	0.544	-0.069	-0.499	-0.304
03	-0.721	0.549	-1.379	0.425
04	-4.561	0.715	0.66	-4.561
05	-4.561	-4.561	1.378	-4.561
06	-4.561	-4.561	-4.561	1.378
07	-4.076	-4.561	-4.561	1.377
08	-0.392	-4.561	1.191	-3.751
09	-4.561	1.378	-4.561	-4.561
10	-4.561	1.378	-4.561	-4.561
11	1.378	-4.561	-4.561	-4.561
12	-4.561	-4.561	-4.561	1.378
13	-4.561	-4.561	1.378	-4.561
14	-4.561	-4.561	1.378	-4.561
15	-4.561	1.324	-4.561	-1.518
16	1.378	-4.561	-4.561	-4.561
17	1.378	-4.561	-4.561	-4.561
18	-4.561	1.378	-4.561	-4.561
19	-0.79	-2.423	1.146	-1.17
20	-0.112	0.15	0.23	-0.378

Standard thresholds

P-value	Threshold
0.001	-10.762485
0.0005	-8.68064
0.0001	-3.93294