RFX5.H12INVITRO.2.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX5.H12INVITRO.2.S.B
Gene (human)	RFX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	16
Consensus	bbGTTGCCATGGbAAC
GC content	52.86%
Information content (bits; total / per base)	20.983 / 1.311
Data sources	HT-SELEX
Aligned words	1566

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	6 (41)	0.736	0.777	0.646	0.687	0.651	0.693	2.207	2.623	84.137	128.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.999	0.999	0.957	0.958	0.85	0.863
Overall, 4 experiments	best	1.0	1.0	0.998	0.998	0.989	0.986
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.991	0.989	0.961	0.953
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.991	0.989	0.961	0.953
Non-Methyl HT-SELEX, 3 experiments	median	1.0	1.0	0.922	0.928	0.74	0.773
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	0.998	0.998	0.989	0.986

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.352	0.252	0.091	0.026

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.622	0.34	0.654	0.453

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: 3.3.3.0.5
HGNC	HGNC:9986
MGI	MGI:1858421
EntrezGene (human)	GeneID:5993 (SSTAR profile)
EntrezGene (mouse)	GeneID:53970 (SSTAR profile)
UniProt ID (human)	RFX5_HUMAN
UniProt ID (mouse)	RFX5_MOUSE
UniProt AC (human)	P48382 (TFClass)
UniProt AC (mouse)	Q9JL61 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	6 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	RFX5.H12INVITRO.2.S.B.pcm
PWM	RFX5.H12INVITRO.2.S.B.pwm
PFM	RFX5.H12INVITRO.2.S.B.pfm
Alignment	RFX5.H12INVITRO.2.S.B.words.tsv
Threshold to P-value map	RFX5.H12INVITRO.2.S.B.thr
Motif in other formats
JASPAR format	RFX5.H12INVITRO.2.S.B_jaspar_format.txt
MEME format	RFX5.H12INVITRO.2.S.B_meme_format.meme
Transfac format	RFX5.H12INVITRO.2.S.B_transfac_format.txt
Homer format	RFX5.H12INVITRO.2.S.B_homer_format_0.001.txt RFX5.H12INVITRO.2.S.B_homer_format_0.0005.txt RFX5.H12INVITRO.2.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	253.75	622.75	386.75	302.75
02	98.0	828.0	471.0	169.0
03	3.0	1.0	1558.0	4.0
04	2.0	1.0	4.0	1559.0
05	11.0	3.0	0.0	1552.0
06	178.0	5.0	1374.0	9.0
07	0.0	1560.0	1.0	5.0
08	0.0	1005.0	6.0	555.0
09	1506.0	2.0	11.0	47.0
10	65.0	18.0	34.0	1449.0
11	94.0	6.0	1457.0	9.0
12	61.0	39.0	1432.0	34.0
13	134.0	657.0	135.0	640.0
14	1361.0	32.0	107.0	66.0
15	1374.75	54.75	59.75	76.75
16	77.25	1322.25	50.25	116.25

PFM

	A	C	G	T
01	0.162	0.398	0.247	0.193
02	0.063	0.529	0.301	0.108
03	0.002	0.001	0.995	0.003
04	0.001	0.001	0.003	0.996
05	0.007	0.002	0.0	0.991
06	0.114	0.003	0.877	0.006
07	0.0	0.996	0.001	0.003
08	0.0	0.642	0.004	0.354
09	0.962	0.001	0.007	0.03
10	0.042	0.011	0.022	0.925
11	0.06	0.004	0.93	0.006
12	0.039	0.025	0.914	0.022
13	0.086	0.42	0.086	0.409
14	0.869	0.02	0.068	0.042
15	0.878	0.035	0.038	0.049
16	0.049	0.844	0.032	0.074

PWM

	A	C	G	T
01	-0.431	0.462	-0.012	-0.256
02	-1.371	0.747	0.184	-0.834
03	-4.398	-4.931	1.378	-4.21
04	-4.629	-4.931	-4.21	1.378
05	-3.422	-4.398	-5.365	1.374
06	-0.783	-4.052	1.252	-3.592
07	-5.365	1.379	-4.931	-4.052
08	-5.365	0.94	-3.916	0.348
09	1.344	-4.629	-3.422	-2.086
10	-1.772	-2.987	-2.396	1.305
11	-1.412	-3.916	1.311	-3.592
12	-1.834	-2.265	1.293	-2.396
13	-1.063	0.516	-1.056	0.49
14	1.243	-2.453	-1.285	-1.758
15	1.253	-1.939	-1.854	-1.61
16	-1.604	1.214	-2.022	-1.203

Standard thresholds

P-value	Threshold
0.001	-1.20839
0.0005	0.40401
0.0001	3.80656