RFX5.H12CORE.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX5.H12CORE.1.PSM.A
Gene (human)	RFX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	12
Consensus	YdGTTRCYRKGb
GC content	56.42%
Information content (bits; total / per base)	11.128 / 0.927
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1001

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)	0.827	0.886	0.765	0.842	0.812	0.867	3.182	3.838	214.824	418.201

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.99	0.983	0.944	0.939	0.844	0.855
Overall, 4 experiments	best	0.995	0.991	0.993	0.988	0.986	0.979
Methyl HT-SELEX, 1 experiments	median	0.991	0.984	0.986	0.977	0.972	0.96
Methyl HT-SELEX, 1 experiments	best	0.991	0.984	0.986	0.977	0.972	0.96
Non-Methyl HT-SELEX, 3 experiments	median	0.99	0.983	0.902	0.901	0.716	0.751
Non-Methyl HT-SELEX, 3 experiments	best	0.995	0.991	0.993	0.988	0.986	0.979

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.881	1.744	0.114	0.025

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.69	0.303	0.664	0.476

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.H12CORE.1.PSM.A.pcm
PWM	RFX5.H12CORE.1.PSM.A.pwm
PFM	RFX5.H12CORE.1.PSM.A.pfm
Alignment	RFX5.H12CORE.1.PSM.A.words.tsv
Threshold to P-value map	RFX5.H12CORE.1.PSM.A.thr
Motif in other formats
JASPAR format	RFX5.H12CORE.1.PSM.A_jaspar_format.txt
MEME format	RFX5.H12CORE.1.PSM.A_meme_format.meme
Transfac format	RFX5.H12CORE.1.PSM.A_transfac_format.txt
Homer format	RFX5.H12CORE.1.PSM.A_homer_format_0.001.txt RFX5.H12CORE.1.PSM.A_homer_format_0.0005.txt RFX5.H12CORE.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	54.0	618.0	111.0	218.0
02	241.0	56.0	210.0	494.0
03	14.0	10.0	965.0	12.0
04	10.0	20.0	31.0	940.0
05	58.0	115.0	13.0	815.0
06	159.0	25.0	674.0	143.0
07	12.0	936.0	16.0	37.0
08	6.0	454.0	7.0	534.0
09	714.0	16.0	240.0	31.0
10	146.0	23.0	602.0	230.0
11	41.0	52.0	866.0	42.0
12	118.0	365.0	352.0	166.0

PFM

	A	C	G	T
01	0.054	0.617	0.111	0.218
02	0.241	0.056	0.21	0.494
03	0.014	0.01	0.964	0.012
04	0.01	0.02	0.031	0.939
05	0.058	0.115	0.013	0.814
06	0.159	0.025	0.673	0.143
07	0.012	0.935	0.016	0.037
08	0.006	0.454	0.007	0.533
09	0.713	0.016	0.24	0.031
10	0.146	0.023	0.601	0.23
11	0.041	0.052	0.865	0.042
12	0.118	0.365	0.352	0.166

PWM

	A	C	G	T
01	-1.509	0.9	-0.804	-0.137
02	-0.037	-1.474	-0.174	0.677
03	-2.774	-3.067	1.345	-2.91
04	-3.067	-2.451	-2.041	1.318
05	-1.44	-0.769	-2.84	1.176
06	-0.45	-2.244	0.986	-0.554
07	-2.91	1.314	-2.654	-1.873
08	-3.485	0.593	-3.363	0.754
09	1.044	-2.654	-0.042	-2.041
10	-0.534	-2.321	0.874	-0.084
11	-1.775	-1.545	1.237	-1.751
12	-0.744	0.375	0.339	-0.407

Standard thresholds

P-value	Threshold
0.001	4.438565
0.0005	5.363715
0.0001	7.228225