RFX2.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX2.H12INVIVO.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	YbGTTGCCWKGG
GC content	59.26%
Information content (bits; total / per base)	14.859 / 1.238
Data sources	ChIP-Seq + HT-SELEX
Aligned words	998

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)	0.854	0.962	0.81	0.921	0.876	0.956	4.338	4.642	68.796	533.0
Mouse	2 (14)	0.973	0.985	0.945	0.97	0.971	0.982	5.555	5.952	398.201	607.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.994	0.991	0.871	0.879	0.694	0.732
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	0.998	0.95	0.953
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.998	0.998	0.95	0.953
Non-Methyl HT-SELEX, 5 experiments	median	0.994	0.991	0.855	0.867	0.681	0.722
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	0.873	0.414	0.826	0.477

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.H12INVIVO.0.PS.A.pcm
PWM	RFX2.H12INVIVO.0.PS.A.pwm
PFM	RFX2.H12INVIVO.0.PS.A.pfm
Alignment	RFX2.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	RFX2.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	RFX2.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	RFX2.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	RFX2.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	RFX2.H12INVIVO.0.PS.A_homer_format_0.001.txt RFX2.H12INVIVO.0.PS.A_homer_format_0.0005.txt RFX2.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	38.0	572.0	146.0	242.0
02	69.0	216.0	395.0	318.0
03	2.0	0.0	994.0	2.0
04	0.0	3.0	3.0	992.0
05	3.0	60.0	3.0	932.0
06	29.0	8.0	931.0	30.0
07	1.0	930.0	1.0	66.0
08	0.0	741.0	1.0	256.0
09	803.0	56.0	47.0	92.0
10	137.0	25.0	194.0	642.0
11	66.0	1.0	927.0	4.0
12	150.0	32.0	811.0	5.0

PFM

	A	C	G	T
01	0.038	0.573	0.146	0.242
02	0.069	0.216	0.396	0.319
03	0.002	0.0	0.996	0.002
04	0.0	0.003	0.003	0.994
05	0.003	0.06	0.003	0.934
06	0.029	0.008	0.933	0.03
07	0.001	0.932	0.001	0.066
08	0.0	0.742	0.001	0.257
09	0.805	0.056	0.047	0.092
10	0.137	0.025	0.194	0.643
11	0.066	0.001	0.929	0.004
12	0.15	0.032	0.813	0.005

PWM

	A	C	G	T
01	-1.844	0.826	-0.531	-0.03
02	-1.268	-0.143	0.457	0.241
03	-4.211	-4.98	1.377	-4.211
04	-4.98	-3.973	-3.973	1.375
05	-3.973	-1.404	-3.973	1.313
06	-2.101	-3.252	1.312	-2.069
07	-4.523	1.311	-4.523	-1.311
08	-4.98	1.084	-4.523	0.026
09	1.164	-1.471	-1.64	-0.986
10	-0.594	-2.241	-0.25	0.941
11	-1.311	-4.523	1.307	-3.781
12	-0.504	-2.008	1.174	-3.62

Standard thresholds

P-value	Threshold
0.001	2.66201
0.0005	3.948905
0.0001	6.599225