RFX3.H13RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX3.H13RSNP.0.PSM.A
Gene (human)	RFX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx3
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	22
Consensus	nbbGTTGCCATGGCAACGvndn
GC content	56.35%
Information content (bits; total / per base)	28.166 / 1.28
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	411
Previous names	RFX3.H12RSNP.0.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	1 (7)	0.594	0.605	0.524	0.544	0.884	0.886	5.468	5.58	555.036	586.921
Mouse	1 (5)	0.594	0.596	0.527	0.53	0.891	0.895	5.775	5.802	634.0	718.509

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.657	0.681	0.566	0.589	0.528	0.549
Overall, 6 experiments	best	1	1	1.0	1.0	0.928	0.937
Methyl HT-SELEX, 1 experiments	median	1	1	1.0	1.0	0.928	0.937
Methyl HT-SELEX, 1 experiments	best	1	1	1.0	1.0	0.928	0.937
Non-Methyl HT-SELEX, 5 experiments	median	0.599	0.627	0.541	0.56	0.517	0.533
Non-Methyl HT-SELEX, 5 experiments	best	1	1	1.0	1.0	0.884	0.9

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.799	0.562	0.845	0.68

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

PCM	RFX3.H13RSNP.0.PSM.A.pcm
PWM	RFX3.H13RSNP.0.PSM.A.pwm
PFM	RFX3.H13RSNP.0.PSM.A.pfm
Threshold to P-value map	RFX3.H13RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	RFX3.H13RSNP.0.PSM.A_jaspar_format.txt
MEME format	RFX3.H13RSNP.0.PSM.A_meme_format.meme
Transfac format	RFX3.H13RSNP.0.PSM.A_transfac_format.txt
Homer format	RFX3.H13RSNP.0.PSM.A_homer_format_0.001.txt RFX3.H13RSNP.0.PSM.A_homer_format_0.0005.txt RFX3.H13RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	126.0	67.0	146.0	72.0
02	59.25	112.25	69.25	170.25
03	22.0	140.0	194.0	55.0
04	0.0	1.0	410.0	0.0
05	0.0	0.0	0.0	411.0
06	2.0	0.0	0.0	409.0
07	26.0	0.0	383.0	2.0
08	0.0	397.0	0.0	14.0
09	0.0	399.0	0.0	12.0
10	411.0	0.0	0.0	0.0
11	0.0	0.0	0.0	411.0
12	1.0	0.0	410.0	0.0
13	12.0	0.0	399.0	0.0
14	3.0	292.0	0.0	116.0
15	399.0	0.0	5.0	7.0
16	411.0	0.0	0.0	0.0
17	0.0	411.0	0.0	0.0
18	14.0	39.0	348.0	10.0
19	102.0	64.0	198.0	47.0
20	69.0	71.0	140.0	131.0
21	154.25	17.25	169.25	70.25
22	80.25	79.25	134.25	117.25

PFM

	A	C	G	T
01	0.307	0.163	0.355	0.175
02	0.144	0.273	0.168	0.414
03	0.054	0.341	0.472	0.134
04	0.0	0.002	0.998	0.0
05	0.0	0.0	0.0	1.0
06	0.005	0.0	0.0	0.995
07	0.063	0.0	0.932	0.005
08	0.0	0.966	0.0	0.034
09	0.0	0.971	0.0	0.029
10	1.0	0.0	0.0	0.0
11	0.0	0.0	0.0	1.0
12	0.002	0.0	0.998	0.0
13	0.029	0.0	0.971	0.0
14	0.007	0.71	0.0	0.282
15	0.971	0.0	0.012	0.017
16	1.0	0.0	0.0	0.0
17	0.0	1.0	0.0	0.0
18	0.034	0.095	0.847	0.024
19	0.248	0.156	0.482	0.114
20	0.168	0.173	0.341	0.319
21	0.375	0.042	0.412	0.171
22	0.195	0.193	0.327	0.285

PWM

	A	C	G	T
01	0.201	-0.42	0.347	-0.349
02	-0.54	0.087	-0.388	0.499
03	-1.49	0.305	0.629	-0.613
04	-4.238	-3.729	1.373	-4.238
05	-4.238	-4.238	-4.238	1.375
06	-3.393	-4.238	-4.238	1.371
07	-1.332	-4.238	1.305	-3.393
08	-4.238	1.341	-4.238	-1.906
09	-4.238	1.346	-4.238	-2.044
10	1.375	-4.238	-4.238	-4.238
11	-4.238	-4.238	-4.238	1.375
12	-3.729	-4.238	1.373	-4.238
13	-2.044	-4.238	1.346	-4.238
14	-3.142	1.035	-4.238	0.12
15	1.346	-4.238	-2.774	-2.506
16	1.375	-4.238	-4.238	-4.238
17	-4.238	1.375	-4.238	-4.238
18	-1.906	-0.945	1.21	-2.204
19	-0.007	-0.465	0.649	-0.765
20	-0.391	-0.363	0.305	0.24
21	0.401	-1.715	0.493	-0.374
22	-0.243	-0.255	0.264	0.13

Standard thresholds

P-value	Threshold
0.001	-6.93874
0.0005	-4.99164
0.0001	-0.82229