RFX2.H12INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX2.H12INVITRO.1.PSM.A
Gene (human)	RFX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	16
Consensus	bGTTRCCATGGhdAYn
GC content	49.66%
Information content (bits; total / per base)	17.695 / 1.106
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9788

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)	0.845	0.951	0.825	0.919	0.866	0.94	5.525	5.857	70.959	496.538
Mouse	2 (14)	0.963	0.979	0.941	0.966	0.961	0.982	7.09	8.009	357.146	593.276

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	1.0	0.999	0.869	0.881	0.694	0.733
Overall, 6 experiments	best	1	1	1.0	1.0	1.0	1.0
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	1.0	0.956	0.959
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	1.0	0.956	0.959
Non-Methyl HT-SELEX, 5 experiments	median	0.999	0.999	0.851	0.869	0.675	0.72
Non-Methyl HT-SELEX, 5 experiments	best	1	1	1.0	1.0	1.0	1.0

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.901	0.485	0.864	0.514

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.1.PSM.A.pcm
PWM	RFX2.H12INVITRO.1.PSM.A.pwm
PFM	RFX2.H12INVITRO.1.PSM.A.pfm
Alignment	RFX2.H12INVITRO.1.PSM.A.words.tsv
Threshold to P-value map	RFX2.H12INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	RFX2.H12INVITRO.1.PSM.A_jaspar_format.txt
MEME format	RFX2.H12INVITRO.1.PSM.A_meme_format.meme
Transfac format	RFX2.H12INVITRO.1.PSM.A_transfac_format.txt
Homer format	RFX2.H12INVITRO.1.PSM.A_homer_format_0.001.txt RFX2.H12INVITRO.1.PSM.A_homer_format_0.0005.txt RFX2.H12INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1396.5	3884.5	2832.5	1674.5
02	37.75	42.75	9674.75	32.75
03	25.0	87.0	32.0	9644.0
04	629.0	54.0	7.0	9098.0
05	2674.0	17.0	6451.0	646.0
06	1.0	9019.0	6.0	762.0
07	0.0	6936.0	23.0	2829.0
08	9534.0	25.0	110.0	119.0
09	440.0	91.0	307.0	8950.0
10	1161.0	57.0	8348.0	222.0
11	943.0	373.0	8400.0	72.0
12	1773.0	2740.0	1157.0	4118.0
13	4924.0	526.0	1765.0	2573.0
14	8829.0	405.0	218.0	336.0
15	767.75	7787.75	175.75	1056.75
16	1951.5	2813.5	3406.5	1616.5

PFM

	A	C	G	T
01	0.143	0.397	0.289	0.171
02	0.004	0.004	0.988	0.003
03	0.003	0.009	0.003	0.985
04	0.064	0.006	0.001	0.93
05	0.273	0.002	0.659	0.066
06	0.0	0.921	0.001	0.078
07	0.0	0.709	0.002	0.289
08	0.974	0.003	0.011	0.012
09	0.045	0.009	0.031	0.914
10	0.119	0.006	0.853	0.023
11	0.096	0.038	0.858	0.007
12	0.181	0.28	0.118	0.421
13	0.503	0.054	0.18	0.263
14	0.902	0.041	0.022	0.034
15	0.078	0.796	0.018	0.108
16	0.199	0.287	0.348	0.165

PWM

	A	C	G	T
01	-0.56	0.462	0.146	-0.379
02	-4.113	-3.996	1.374	-4.247
03	-4.497	-3.312	-4.268	1.371
04	-1.356	-3.773	-5.574	1.313
05	0.089	-4.844	0.969	-1.329
06	-6.61	1.304	-5.688	-1.165
07	-6.972	1.041	-4.573	0.145
08	1.359	-4.497	-3.082	-3.005
09	-1.712	-3.268	-2.069	1.296
10	-0.745	-3.721	1.226	-2.391
11	-0.952	-1.876	1.233	-3.495
12	-0.322	0.113	-0.748	0.52
13	0.699	-1.534	-0.326	0.05
14	1.283	-1.794	-2.409	-1.98
15	-1.157	1.157	-2.622	-0.838
16	-0.226	0.139	0.331	-0.414

Standard thresholds

P-value	Threshold
0.001	0.91311
0.0005	2.36566
0.0001	5.39411