RFX1.H12INVIVO.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX1.H12INVIVO.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	12
Consensus	bbGTTGCCAKGS
GC content	58.3%
Information content (bits; total / per base)	13.642 / 1.137
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	968

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)	0.971	0.991	0.944	0.981	0.959	0.987	5.107	6.134	676.027	897.796
Mouse	4 (20)	0.966	0.975	0.932	0.948	0.951	0.961	4.883	5.538	664.188	811.027

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.988	0.983	0.957	0.948	0.879	0.882
Overall, 4 experiments	best	1.0	1.0	0.999	0.999	0.994	0.993
Methyl HT-SELEX, 2 experiments	median	0.988	0.983	0.957	0.948	0.879	0.882
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.999	0.998	0.988	0.986
Non-Methyl HT-SELEX, 2 experiments	median	0.984	0.971	0.937	0.928	0.853	0.862
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.999	0.999	0.994	0.993

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.363	11.49	0.199	0.1

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.934	0.559	0.891	0.483
batch 2	0.938	0.747	0.829	0.387

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.H12INVIVO.0.PM.A.pcm
PWM	RFX1.H12INVIVO.0.PM.A.pwm
PFM	RFX1.H12INVIVO.0.PM.A.pfm
Alignment	RFX1.H12INVIVO.0.PM.A.words.tsv
Threshold to P-value map	RFX1.H12INVIVO.0.PM.A.thr
Motif in other formats
JASPAR format	RFX1.H12INVIVO.0.PM.A_jaspar_format.txt
MEME format	RFX1.H12INVIVO.0.PM.A_meme_format.meme
Transfac format	RFX1.H12INVIVO.0.PM.A_transfac_format.txt
Homer format	RFX1.H12INVIVO.0.PM.A_homer_format_0.001.txt RFX1.H12INVIVO.0.PM.A_homer_format_0.0005.txt RFX1.H12INVIVO.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	63.0	469.0	184.0	252.0
02	94.0	242.0	380.0	252.0
03	3.0	2.0	961.0	2.0
04	0.0	7.0	4.0	957.0
05	26.0	65.0	3.0	874.0
06	106.0	7.0	783.0	72.0
07	1.0	881.0	3.0	83.0
08	0.0	697.0	0.0	271.0
09	822.0	30.0	60.0	56.0
10	119.0	32.0	208.0	609.0
11	61.0	5.0	894.0	8.0
12	106.0	116.0	739.0	7.0

PFM

	A	C	G	T
01	0.065	0.485	0.19	0.26
02	0.097	0.25	0.393	0.26
03	0.003	0.002	0.993	0.002
04	0.0	0.007	0.004	0.989
05	0.027	0.067	0.003	0.903
06	0.11	0.007	0.809	0.074
07	0.001	0.91	0.003	0.086
08	0.0	0.72	0.0	0.28
09	0.849	0.031	0.062	0.058
10	0.123	0.033	0.215	0.629
11	0.063	0.005	0.924	0.008
12	0.11	0.12	0.763	0.007

PWM

	A	C	G	T
01	-1.326	0.658	-0.272	0.04
02	-0.935	0.0	0.449	0.04
03	-3.944	-4.183	1.374	-4.183
04	-4.954	-3.331	-3.752	1.37
05	-2.174	-1.296	-3.944	1.279
06	-0.816	-3.331	1.169	-1.196
07	-4.496	1.287	-3.944	-1.057
08	-4.954	1.053	-4.954	0.112
09	1.218	-2.039	-1.373	-1.44
10	-0.703	-1.978	-0.15	0.919
11	-1.357	-3.591	1.302	-3.222
12	-0.816	-0.728	1.112	-3.331

Standard thresholds

P-value	Threshold
0.001	3.41252
0.0005	4.59079
0.0001	6.954525