RFX3.H12INVITRO.2.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX3.H12INVITRO.2.S.B
Gene (human)	RFX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx3
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	17
Consensus	dKKTGTAGGTTAGGKdd
GC content	48.44%
Information content (bits; total / per base)	21.68 / 1.275
Data sources	HT-SELEX
Aligned words	296

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	1 (7)	0.398	0.431	0.282	0.297	0.51	0.542	1.047	1.124	0	0
Mouse	1 (5)	0.433	0.438	0.297	0.302	0.547	0.549	1.125	1.132	0	0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.509	0.502	0.513	0.504	0.509	0.504
Overall, 6 experiments	best	0.773	0.771	0.638	0.65	0.563	0.585
Methyl HT-SELEX, 1 experiments	median	0.504	0.504	0.495	0.5	0.483	0.495
Methyl HT-SELEX, 1 experiments	best	0.504	0.504	0.495	0.5	0.483	0.495
Non-Methyl HT-SELEX, 5 experiments	median	0.51	0.5	0.515	0.504	0.51	0.504
Non-Methyl HT-SELEX, 5 experiments	best	0.773	0.771	0.638	0.65	0.563	0.585

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.407	0.018	-0.316	-0.134

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: 3.3.3.0.3
HGNC	HGNC:9984
MGI	MGI:106582
EntrezGene (human)	GeneID:5991 (SSTAR profile)
EntrezGene (mouse)	GeneID:19726 (SSTAR profile)
UniProt ID (human)	RFX3_HUMAN
UniProt ID (mouse)	RFX3_MOUSE
UniProt AC (human)	P48380 (TFClass)
UniProt AC (mouse)	P48381 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 1 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	RFX3.H12INVITRO.2.S.B.pcm
PWM	RFX3.H12INVITRO.2.S.B.pwm
PFM	RFX3.H12INVITRO.2.S.B.pfm
Alignment	RFX3.H12INVITRO.2.S.B.words.tsv
Threshold to P-value map	RFX3.H12INVITRO.2.S.B.thr
Motif in other formats
JASPAR format	RFX3.H12INVITRO.2.S.B_jaspar_format.txt
MEME format	RFX3.H12INVITRO.2.S.B_meme_format.meme
Transfac format	RFX3.H12INVITRO.2.S.B_transfac_format.txt
Homer format	RFX3.H12INVITRO.2.S.B_homer_format_0.001.txt RFX3.H12INVITRO.2.S.B_homer_format_0.0005.txt RFX3.H12INVITRO.2.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	75.25	32.25	111.25	77.25
02	34.25	11.25	208.25	42.25
03	14.0	6.0	50.0	226.0
04	7.0	14.0	21.0	254.0
05	18.0	0.0	270.0	8.0
06	0.0	0.0	20.0	276.0
07	281.0	0.0	13.0	2.0
08	0.0	0.0	294.0	2.0
09	0.0	0.0	293.0	3.0
10	20.0	0.0	12.0	264.0
11	0.0	2.0	6.0	288.0
12	296.0	0.0	0.0	0.0
13	0.0	0.0	295.0	1.0
14	0.0	0.0	292.0	4.0
15	22.0	30.0	193.0	51.0
16	133.0	34.0	72.0	57.0
17	43.25	24.25	133.25	95.25

PFM

	A	C	G	T
01	0.254	0.109	0.376	0.261
02	0.116	0.038	0.704	0.143
03	0.047	0.02	0.169	0.764
04	0.024	0.047	0.071	0.858
05	0.061	0.0	0.912	0.027
06	0.0	0.0	0.068	0.932
07	0.949	0.0	0.044	0.007
08	0.0	0.0	0.993	0.007
09	0.0	0.0	0.99	0.01
10	0.068	0.0	0.041	0.892
11	0.0	0.007	0.02	0.973
12	1.0	0.0	0.0	0.0
13	0.0	0.0	0.997	0.003
14	0.0	0.0	0.986	0.014
15	0.074	0.101	0.652	0.172
16	0.449	0.115	0.243	0.193
17	0.146	0.082	0.45	0.322

PWM

	A	C	G	T
01	0.016	-0.806	0.401	0.042
02	-0.749	-1.784	1.022	-0.546
03	-1.587	-2.319	-0.383	1.104
04	-2.192	-1.587	-1.213	1.22
05	-1.357	-3.971	1.281	-2.08
06	-3.971	-3.971	-1.259	1.302
07	1.32	-3.971	-1.654	-3.093
08	-3.971	-3.971	1.365	-3.093
09	-3.971	-3.971	1.362	-2.836
10	-1.259	-3.971	-1.726	1.258
11	-3.971	-3.093	-2.319	1.345
12	1.372	-3.971	-3.971	-3.971
13	-3.971	-3.971	1.369	-3.438
14	-3.971	-3.971	1.359	-2.633
15	-1.169	-0.876	0.947	-0.364
16	0.578	-0.756	-0.027	-0.255
17	-0.524	-1.078	0.58	0.248

Standard thresholds

P-value	Threshold
0.001	-0.55609
0.0005	0.95486
0.0001	4.16006