RFX2.H14INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX2.H14INVIVO.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	17
Consensus	bbGTTGCCRdGGvRMSv
GC content	60.64%
Information content (bits; total / per base)	15.547 / 0.915
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000
Previous names	RFX2.H12INVIVO.1.PSM.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	2 (13)	0.865	0.979	0.848	0.96	0.886	0.977	5.946	6.488	76.229	594.377
Mouse	2 (14)	0.98	0.992	0.97	0.984	0.978	0.989	7.236	7.572	398.102	615.131

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.999	0.998	0.862	0.876	0.677	0.725
Overall, 6 experiments	best	1	1	1.0	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	1.0	0.952	0.956
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	0.952	0.956
Non-Methyl HT-SELEX, 5 experiments	median	0.998	0.998	0.842	0.863	0.659	0.712
Non-Methyl HT-SELEX, 5 experiments	best	1	1	1.0	1.0	1.0	1.0

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.857	0.349	0.853	0.484

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	RFX2.H14INVIVO.1.PSM.A.pcm
PWM	RFX2.H14INVIVO.1.PSM.A.pwm
PFM	RFX2.H14INVIVO.1.PSM.A.pfm
Threshold to P-value map	RFX2.H14INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	RFX2.H14INVIVO.1.PSM.A_jaspar_format.txt
MEME format	RFX2.H14INVIVO.1.PSM.A_meme_format.meme
Transfac format	RFX2.H14INVIVO.1.PSM.A_transfac_format.txt
Homer format	RFX2.H14INVIVO.1.PSM.A_homer_format_0.001.txt RFX2.H14INVIVO.1.PSM.A_homer_format_0.0005.txt RFX2.H14INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	53.0	545.0	196.0	206.0
02	113.0	355.0	392.0	140.0
03	7.0	0.0	991.0	2.0
04	6.0	19.0	4.0	971.0
05	25.0	91.0	11.0	873.0
06	105.0	10.0	834.0	51.0
07	1.0	943.0	0.0	56.0
08	0.0	693.0	2.0	305.0
09	748.0	70.0	104.0	78.0
10	165.0	50.0	269.0	516.0
11	39.0	5.0	950.0	6.0
12	140.0	78.0	777.0	5.0
13	277.0	371.0	207.0	145.0
14	454.0	50.0	435.0	61.0
15	687.0	190.0	86.0	37.0
16	73.0	753.0	95.0	79.0
17	177.0	345.0	387.0	91.0

PFM

	A	C	G	T
01	0.053	0.545	0.196	0.206
02	0.113	0.355	0.392	0.14
03	0.007	0.0	0.991	0.002
04	0.006	0.019	0.004	0.971
05	0.025	0.091	0.011	0.873
06	0.105	0.01	0.834	0.051
07	0.001	0.943	0.0	0.056
08	0.0	0.693	0.002	0.305
09	0.748	0.07	0.104	0.078
10	0.165	0.05	0.269	0.516
11	0.039	0.005	0.95	0.006
12	0.14	0.078	0.777	0.005
13	0.277	0.371	0.207	0.145
14	0.454	0.05	0.435	0.061
15	0.687	0.19	0.086	0.037
16	0.073	0.753	0.095	0.079
17	0.177	0.345	0.387	0.091

PWM

	A	C	G	T
01	-1.526	0.776	-0.241	-0.192
02	-0.786	0.349	0.447	-0.574
03	-3.362	-4.982	1.372	-4.213
04	-3.484	-2.497	-3.783	1.352
05	-2.243	-0.999	-2.985	1.246
06	-0.858	-3.066	1.2	-1.563
07	-4.525	1.323	-4.982	-1.473
08	-4.982	1.015	-4.213	0.198
09	1.091	-1.255	-0.867	-1.15
10	-0.412	-1.582	0.073	0.721
11	-1.821	-3.622	1.33	-3.484
12	-0.574	-1.15	1.129	-3.622
13	0.102	0.393	-0.187	-0.54
14	0.594	-1.582	0.551	-1.39
15	1.006	-0.272	-1.054	-1.872
16	-1.215	1.098	-0.956	-1.137
17	-0.342	0.32	0.435	-0.999

Standard thresholds

P-value	Threshold
0.001	2.73911
0.0005	3.95046
0.0001	6.46221