RFX5.H12CORE.2.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX5.H12CORE.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	18
Consensus	nbSGTTGCCATGGYAACv
GC content	54.59%
Information content (bits; total / per base)	22.292 / 1.238
Data sources	HT-SELEX
Aligned words	9183

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)	0.745	0.785	0.656	0.699	0.661	0.705	2.223	2.645	78.585	119.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.999	0.999	0.956	0.958	0.852	0.865
Overall, 4 experiments	best	1.0	1.0	0.998	0.998	0.991	0.988
Methyl HT-SELEX, 1 experiments	median	0.999	0.999	0.992	0.989	0.965	0.957
Methyl HT-SELEX, 1 experiments	best	0.999	0.999	0.992	0.989	0.965	0.957
Non-Methyl HT-SELEX, 3 experiments	median	1.0	1.0	0.921	0.927	0.739	0.773
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	0.998	0.998	0.991	0.988

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.596	0.492	0.1	0.022

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.643	0.349	0.673	0.449

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.2.S.B.pcm
PWM	RFX5.H12CORE.2.S.B.pwm
PFM	RFX5.H12CORE.2.S.B.pfm
Alignment	RFX5.H12CORE.2.S.B.words.tsv
Threshold to P-value map	RFX5.H12CORE.2.S.B.thr
Motif in other formats
JASPAR format	RFX5.H12CORE.2.S.B_jaspar_format.txt
MEME format	RFX5.H12CORE.2.S.B_meme_format.meme
Transfac format	RFX5.H12CORE.2.S.B_transfac_format.txt
Homer format	RFX5.H12CORE.2.S.B_homer_format_0.001.txt RFX5.H12CORE.2.S.B_homer_format_0.0005.txt RFX5.H12CORE.2.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2458.0	2713.0	1922.0	2090.0
02	1142.75	4235.75	1989.75	1814.75
03	470.0	4711.0	3163.0	839.0
04	12.0	0.0	9157.0	14.0
05	8.0	8.0	2.0	9165.0
06	4.0	5.0	1.0	9173.0
07	443.0	3.0	8727.0	10.0
08	1.0	9164.0	0.0	18.0
09	3.0	5814.0	11.0	3355.0
10	9040.0	4.0	18.0	121.0
11	186.0	52.0	108.0	8837.0
12	540.0	54.0	8564.0	25.0
13	135.0	355.0	8512.0	181.0
14	540.0	4413.0	633.0	3597.0
15	7993.0	224.0	396.0	570.0
16	8099.0	226.0	329.0	529.0
17	370.25	7841.25	426.25	545.25
18	1671.0	2924.0	3523.0	1065.0

PFM

	A	C	G	T
01	0.268	0.295	0.209	0.228
02	0.124	0.461	0.217	0.198
03	0.051	0.513	0.344	0.091
04	0.001	0.0	0.997	0.002
05	0.001	0.001	0.0	0.998
06	0.0	0.001	0.0	0.999
07	0.048	0.0	0.95	0.001
08	0.0	0.998	0.0	0.002
09	0.0	0.633	0.001	0.365
10	0.984	0.0	0.002	0.013
11	0.02	0.006	0.012	0.962
12	0.059	0.006	0.933	0.003
13	0.015	0.039	0.927	0.02
14	0.059	0.481	0.069	0.392
15	0.87	0.024	0.043	0.062
16	0.882	0.025	0.036	0.058
17	0.04	0.854	0.046	0.059
18	0.182	0.318	0.384	0.116

PWM

	A	C	G	T
01	0.068	0.167	-0.178	-0.094
02	-0.697	0.612	-0.143	-0.235
03	-1.582	0.718	0.32	-1.005
04	-5.081	-6.915	1.383	-4.95
05	-5.409	-5.409	-6.286	1.384
06	-5.902	-5.755	-6.552	1.384
07	-1.641	-6.076	1.335	-5.232
08	-6.552	1.383	-6.915	-4.73
09	-6.076	0.929	-5.153	0.379
10	1.37	-5.902	-4.73	-2.925
11	-2.502	-3.746	-3.037	1.347
12	-1.444	-3.709	1.316	-4.434
13	-2.818	-1.861	1.31	-2.529
14	-1.444	0.653	-1.286	0.449
15	1.247	-2.318	-1.753	-1.39
16	1.26	-2.309	-1.937	-1.465
17	-1.819	1.228	-1.679	-1.434
18	-0.317	0.242	0.428	-0.767

Standard thresholds

P-value	Threshold
0.001	-3.84169
0.0005	-1.92384
0.0001	2.10751