RFX1.H12INVITRO.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX1.H12INVITRO.0.PM.A
Gene (human)	RFX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	15
Consensus	nbGTTGCCATGGYdd
GC content	52.11%
Information content (bits; total / per base)	15.568 / 1.038
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	2500

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	5 (35)	0.954	0.98	0.922	0.97	0.937	0.972	5.656	7.39	638.398	879.854
Mouse	4 (20)	0.949	0.959	0.917	0.936	0.934	0.951	5.379	6.333	613.549	826.174

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.997	0.996	0.971	0.968	0.891	0.897
Overall, 4 experiments	best	1.0	1.0	1.0	1.0	0.994	0.994
Methyl HT-SELEX, 2 experiments	median	0.997	0.996	0.971	0.968	0.891	0.897
Methyl HT-SELEX, 2 experiments	best	1.0	1.0	1.0	1.0	0.991	0.991
Non-Methyl HT-SELEX, 2 experiments	median	0.879	0.871	0.82	0.82	0.783	0.789
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	1.0	1.0	0.994	0.994

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.591	7.777	0.175	0.093

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.955	0.598	0.92	0.565
batch 2	0.881	0.733	0.789	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: 3.3.3.0.1
HGNC	HGNC:9982
MGI	MGI:105982
EntrezGene (human)	GeneID:5989 (SSTAR profile)
EntrezGene (mouse)	GeneID:19724 (SSTAR profile)
UniProt ID (human)	RFX1_HUMAN
UniProt ID (mouse)	RFX1_MOUSE
UniProt AC (human)	P22670 (TFClass)
UniProt AC (mouse)	P48377 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 4 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	RFX1.H12INVITRO.0.PM.A.pcm
PWM	RFX1.H12INVITRO.0.PM.A.pwm
PFM	RFX1.H12INVITRO.0.PM.A.pfm
Alignment	RFX1.H12INVITRO.0.PM.A.words.tsv
Threshold to P-value map	RFX1.H12INVITRO.0.PM.A.thr
Motif in other formats
JASPAR format	RFX1.H12INVITRO.0.PM.A_jaspar_format.txt
MEME format	RFX1.H12INVITRO.0.PM.A_meme_format.meme
Transfac format	RFX1.H12INVITRO.0.PM.A_transfac_format.txt
Homer format	RFX1.H12INVITRO.0.PM.A_homer_format_0.001.txt RFX1.H12INVITRO.0.PM.A_homer_format_0.0005.txt RFX1.H12INVITRO.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	454.25	627.25	615.25	803.25
02	229.25	1113.25	728.25	429.25
03	61.0	5.0	2419.0	15.0
04	13.0	16.0	5.0	2466.0
05	90.0	172.0	6.0	2232.0
06	343.0	9.0	2074.0	74.0
07	2.0	2296.0	2.0	200.0
08	0.0	2103.0	2.0	395.0
09	2296.0	17.0	132.0	55.0
10	100.0	138.0	71.0	2191.0
11	220.0	49.0	2176.0	55.0
12	212.0	70.0	2178.0	40.0
13	193.0	607.0	261.0	1439.0
14	915.0	318.0	606.0	661.0
15	1398.25	348.25	377.25	376.25

PFM

	A	C	G	T
01	0.182	0.251	0.246	0.321
02	0.092	0.445	0.291	0.172
03	0.024	0.002	0.968	0.006
04	0.005	0.006	0.002	0.986
05	0.036	0.069	0.002	0.893
06	0.137	0.004	0.83	0.03
07	0.001	0.918	0.001	0.08
08	0.0	0.841	0.001	0.158
09	0.918	0.007	0.053	0.022
10	0.04	0.055	0.028	0.876
11	0.088	0.02	0.87	0.022
12	0.085	0.028	0.871	0.016
13	0.077	0.243	0.104	0.576
14	0.366	0.127	0.242	0.264
15	0.559	0.139	0.151	0.151

PWM

	A	C	G	T
01	-0.318	0.004	-0.016	0.25
02	-0.998	0.576	0.152	-0.374
03	-2.298	-4.501	1.351	-3.61
04	-3.736	-3.553	-4.501	1.37
05	-1.92	-1.282	-4.367	1.271
06	-0.597	-4.047	1.197	-2.111
07	-5.066	1.299	-5.066	-1.133
08	-5.77	1.211	-5.066	-0.457
09	1.299	-3.499	-1.543	-2.399
10	-1.816	-1.5	-2.151	1.252
11	-1.038	-2.51	1.245	-2.399
12	-1.075	-2.165	1.246	-2.704
13	-1.168	-0.029	-0.869	0.832
14	0.38	-0.673	-0.031	0.056
15	0.803	-0.582	-0.503	-0.505

Standard thresholds

P-value	Threshold
0.001	2.53756
0.0005	3.78096
0.0001	6.36306