RFX1.H12INVITRO.2.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX1.H12INVITRO.2.S.C
Gene (human)	RFX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	11
Consensus	nnSGTTGCYdn
GC content	54.69%
Information content (bits; total / per base)	11.032 / 1.003
Data sources	HT-SELEX
Aligned words	731

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)	0.857	0.892	0.775	0.817	0.766	0.8	2.228	2.419	384.155	515.086
Mouse	4 (20)	0.835	0.855	0.721	0.74	0.749	0.778	2.137	2.247	366.235	424.143

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.958	0.94	0.88	0.864	0.782	0.775
Overall, 4 experiments	best	0.985	0.977	0.976	0.962	0.919	0.905
Methyl HT-SELEX, 2 experiments	median	0.899	0.86	0.838	0.81	0.764	0.744
Methyl HT-SELEX, 2 experiments	best	0.97	0.951	0.956	0.931	0.879	0.857
Non-Methyl HT-SELEX, 2 experiments	median	0.966	0.953	0.89	0.88	0.802	0.799
Non-Methyl HT-SELEX, 2 experiments	best	0.985	0.977	0.976	0.962	0.919	0.905

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.369	6.321	0.131	0.052

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.666	0.193	0.632	0.457
batch 2	0.618	0.333	0.757	0.52

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.2.S.C.pcm
PWM	RFX1.H12INVITRO.2.S.C.pwm
PFM	RFX1.H12INVITRO.2.S.C.pfm
Alignment	RFX1.H12INVITRO.2.S.C.words.tsv
Threshold to P-value map	RFX1.H12INVITRO.2.S.C.thr
Motif in other formats
JASPAR format	RFX1.H12INVITRO.2.S.C_jaspar_format.txt
MEME format	RFX1.H12INVITRO.2.S.C_meme_format.meme
Transfac format	RFX1.H12INVITRO.2.S.C_transfac_format.txt
Homer format	RFX1.H12INVITRO.2.S.C_homer_format_0.001.txt RFX1.H12INVITRO.2.S.C_homer_format_0.0005.txt RFX1.H12INVITRO.2.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	206.75	146.75	241.75	135.75
02	183.25	112.25	255.25	180.25
03	28.0	317.0	311.0	75.0
04	0.0	0.0	731.0	0.0
05	0.0	0.0	5.0	726.0
06	3.0	0.0	0.0	728.0
07	3.0	0.0	728.0	0.0
08	0.0	698.0	32.0	1.0
09	2.0	154.0	81.0	494.0
10	305.75	116.75	132.75	175.75
11	153.75	145.75	189.75	241.75

PFM

	A	C	G	T
01	0.283	0.201	0.331	0.186
02	0.251	0.154	0.349	0.247
03	0.038	0.434	0.425	0.103
04	0.0	0.0	1.0	0.0
05	0.0	0.0	0.007	0.993
06	0.004	0.0	0.0	0.996
07	0.004	0.0	0.996	0.0
08	0.0	0.955	0.044	0.001
09	0.003	0.211	0.111	0.676
10	0.418	0.16	0.182	0.24
11	0.21	0.199	0.26	0.331

PWM

	A	C	G	T
01	0.122	-0.217	0.278	-0.294
02	0.003	-0.482	0.332	-0.014
03	-1.828	0.547	0.528	-0.878
04	-4.717	-4.717	1.38	-4.717
05	-4.717	-4.717	-3.323	1.373
06	-3.681	-4.717	-4.717	1.375
07	-3.681	-4.717	1.375	-4.717
08	-4.717	1.333	-1.701	-4.243
09	-3.923	-0.169	-0.803	0.989
10	0.511	-0.443	-0.316	-0.039
11	-0.171	-0.224	0.037	0.278

Standard thresholds

P-value	Threshold
0.001	3.937165
0.0005	5.727605
0.0001	7.86294