RFX5.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX5.H12INVIVO.1.PSM.A
Gene (human)	RFX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	12
Consensus	YdGTTRCYRKGb
GC content	56.49%
Information content (bits; total / per base)	11.224 / 0.935
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1002

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)	0.827	0.887	0.766	0.846	0.811	0.868	3.171	3.849	213.174	419.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.99	0.982	0.944	0.938	0.844	0.855
Overall, 4 experiments	best	0.995	0.991	0.993	0.988	0.985	0.978
Methyl HT-SELEX, 1 experiments	median	0.99	0.983	0.986	0.976	0.972	0.959
Methyl HT-SELEX, 1 experiments	best	0.99	0.983	0.986	0.976	0.972	0.959
Non-Methyl HT-SELEX, 3 experiments	median	0.989	0.982	0.901	0.899	0.715	0.75
Non-Methyl HT-SELEX, 3 experiments	best	0.995	0.991	0.993	0.988	0.985	0.978

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.946	1.749	0.11	0.027

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.685	0.31	0.663	0.468

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.H12INVIVO.1.PSM.A.pcm
PWM	RFX5.H12INVIVO.1.PSM.A.pwm
PFM	RFX5.H12INVIVO.1.PSM.A.pfm
Alignment	RFX5.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	RFX5.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	RFX5.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	RFX5.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	RFX5.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	RFX5.H12INVIVO.1.PSM.A_homer_format_0.001.txt RFX5.H12INVIVO.1.PSM.A_homer_format_0.0005.txt RFX5.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	51.0	625.0	111.0	215.0
02	249.0	53.0	191.0	509.0
03	15.0	8.0	964.0	15.0
04	13.0	19.0	24.0	946.0
05	49.0	117.0	12.0	824.0
06	155.0	29.0	691.0	127.0
07	10.0	935.0	16.0	41.0
08	5.0	450.0	11.0	536.0
09	707.0	15.0	251.0	29.0
10	148.0	24.0	605.0	225.0
11	46.0	52.0	864.0	40.0
12	110.0	371.0	354.0	167.0

PFM

	A	C	G	T
01	0.051	0.624	0.111	0.215
02	0.249	0.053	0.191	0.508
03	0.015	0.008	0.962	0.015
04	0.013	0.019	0.024	0.944
05	0.049	0.117	0.012	0.822
06	0.155	0.029	0.69	0.127
07	0.01	0.933	0.016	0.041
08	0.005	0.449	0.011	0.535
09	0.706	0.015	0.25	0.029
10	0.148	0.024	0.604	0.225
11	0.046	0.052	0.862	0.04
12	0.11	0.37	0.353	0.167

PWM

	A	C	G	T
01	-1.565	0.91	-0.805	-0.152
02	-0.006	-1.528	-0.269	0.706
03	-2.713	-3.255	1.343	-2.713
04	-2.841	-2.499	-2.283	1.324
05	-1.604	-0.754	-2.911	1.186
06	-0.476	-2.105	1.01	-0.673
07	-3.068	1.312	-2.655	-1.775
08	-3.624	0.583	-2.987	0.757
09	1.033	-2.713	0.002	-2.105
10	-0.522	-2.283	0.878	-0.107
11	-1.665	-1.546	1.233	-1.799
12	-0.814	0.391	0.344	-0.402

Standard thresholds

P-value	Threshold
0.001	4.403565
0.0005	5.33252
0.0001	7.219385