RFX2.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX2.H12INVITRO.0.PS.A
Gene (human)	RFX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	14
Consensus	nbGTTRCCATGRYn
GC content	51.5%
Information content (bits; total / per base)	13.901 / 0.993
Data sources	ChIP-Seq + HT-SELEX
Aligned words	9977

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	2 (13)	0.846	0.951	0.819	0.911	0.867	0.936	4.377	4.581	62.699	493.208
Mouse	2 (14)	0.963	0.978	0.935	0.961	0.961	0.976	5.662	6.375	375.074	593.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.998	0.997	0.876	0.886	0.699	0.737
Overall, 6 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	0.999	0.955	0.957
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	0.999	0.955	0.957
Non-Methyl HT-SELEX, 5 experiments	median	0.997	0.996	0.857	0.872	0.682	0.724
Non-Methyl HT-SELEX, 5 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.892	0.449	0.848	0.493

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: 3.3.3.0.2
HGNC	HGNC:9983
MGI	MGI:106583
EntrezGene (human)	GeneID:5990 (SSTAR profile)
EntrezGene (mouse)	GeneID:19725 (SSTAR profile)
UniProt ID (human)	RFX2_HUMAN
UniProt ID (mouse)	RFX2_MOUSE
UniProt AC (human)	P48378 (TFClass)
UniProt AC (mouse)	P48379 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 2 mouse
HT-SELEX	5
Methyl-HT-SELEX	1

PCM	RFX2.H12INVITRO.0.PS.A.pcm
PWM	RFX2.H12INVITRO.0.PS.A.pwm
PFM	RFX2.H12INVITRO.0.PS.A.pfm
Alignment	RFX2.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	RFX2.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	RFX2.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	RFX2.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	RFX2.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	RFX2.H12INVITRO.0.PS.A_homer_format_0.001.txt RFX2.H12INVITRO.0.PS.A_homer_format_0.0005.txt RFX2.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1519.75	2946.75	1967.75	3542.75
02	990.0	3757.0	3350.0	1880.0
03	106.0	32.0	9768.0	71.0
04	40.0	66.0	21.0	9850.0
05	802.0	134.0	8.0	9033.0
06	2814.0	16.0	6310.0	837.0
07	1.0	9067.0	11.0	898.0
08	7.0	6110.0	23.0	3837.0
09	9596.0	77.0	71.0	233.0
10	860.0	226.0	601.0	8290.0
11	998.0	171.0	8494.0	314.0
12	2145.0	1098.0	6419.0	315.0
13	1384.0	6298.0	842.0	1453.0
14	3648.0	2018.0	2029.0	2282.0

PFM

	A	C	G	T
01	0.152	0.295	0.197	0.355
02	0.099	0.377	0.336	0.188
03	0.011	0.003	0.979	0.007
04	0.004	0.007	0.002	0.987
05	0.08	0.013	0.001	0.905
06	0.282	0.002	0.632	0.084
07	0.0	0.909	0.001	0.09
08	0.001	0.612	0.002	0.385
09	0.962	0.008	0.007	0.023
10	0.086	0.023	0.06	0.831
11	0.1	0.017	0.851	0.031
12	0.215	0.11	0.643	0.032
13	0.139	0.631	0.084	0.146
14	0.366	0.202	0.203	0.229

PWM

	A	C	G	T
01	-0.495	0.167	-0.237	0.351
02	-0.923	0.409	0.295	-0.282
03	-3.138	-4.287	1.364	-3.528
04	-4.078	-3.599	-4.674	1.373
05	-1.133	-2.908	-5.49	1.286
06	0.121	-4.916	0.928	-1.09
07	-6.628	1.29	-5.235	-1.02
08	-5.592	0.895	-4.592	0.43
09	1.347	-3.449	-3.528	-2.362
10	-1.063	-2.392	-1.42	1.2
11	-0.915	-2.668	1.225	-2.066
12	-0.151	-0.819	0.945	-2.063
13	-0.588	0.926	-1.084	-0.54
14	0.38	-0.212	-0.206	-0.089

Standard thresholds

P-value	Threshold
0.001	3.08526
0.0005	4.31681
0.0001	6.835465