TFCP2.H12INVIVO.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TFCP2.H12INVIVO.1.SM.D
Gene (human)	TFCP2 (GeneCards)
Gene synonyms (human)	LSF, SEF
Gene (mouse)	Tfcp2
Gene synonyms (mouse)	Tcfcp2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	21
Consensus	nvRWCCGGYYdRAACCGGWWn
GC content	50.63%
Information content (bits; total / per base)	19.316 / 0.92
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	454

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.991	0.986	0.976	0.966	0.929	0.914
Overall, 5 experiments	best	1.0	0.999	0.999	0.998	0.997	0.996
Methyl HT-SELEX, 2 experiments	median	0.995	0.993	0.987	0.982	0.962	0.954
Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.999	0.998	0.995	0.994
Non-Methyl HT-SELEX, 3 experiments	median	0.957	0.949	0.781	0.791	0.641	0.674
Non-Methyl HT-SELEX, 3 experiments	best	1.0	0.999	0.999	0.998	0.997	0.996

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.903	0.776	0.914	0.628
batch 2	0.733	0.218	0.826	0.554

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	Grainyhead domain factors {6.7} (TFClass)
TF family	CP2-related {6.7.2} (TFClass)
TF subfamily	{6.7.2.0} (TFClass)
TFClass ID	TFClass: 6.7.2.0.1
HGNC	HGNC:11748
MGI	MGI:98509
EntrezGene (human)	GeneID:7024 (SSTAR profile)
EntrezGene (mouse)	GeneID:21422 (SSTAR profile)
UniProt ID (human)	TFCP2_HUMAN
UniProt ID (mouse)	TFCP2_MOUSE
UniProt AC (human)	Q12800 (TFClass)
UniProt AC (mouse)	Q9ERA0 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	2

PCM	TFCP2.H12INVIVO.1.SM.D.pcm
PWM	TFCP2.H12INVIVO.1.SM.D.pwm
PFM	TFCP2.H12INVIVO.1.SM.D.pfm
Alignment	TFCP2.H12INVIVO.1.SM.D.words.tsv
Threshold to P-value map	TFCP2.H12INVIVO.1.SM.D.thr
Motif in other formats
JASPAR format	TFCP2.H12INVIVO.1.SM.D_jaspar_format.txt
MEME format	TFCP2.H12INVIVO.1.SM.D_meme_format.meme
Transfac format	TFCP2.H12INVIVO.1.SM.D_transfac_format.txt
Homer format	TFCP2.H12INVIVO.1.SM.D_homer_format_0.001.txt TFCP2.H12INVIVO.1.SM.D_homer_format_0.0005.txt TFCP2.H12INVIVO.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	121.0	122.0	95.0	116.0
02	177.25	65.25	161.25	50.25
03	306.0	14.0	68.0	66.0
04	295.0	6.0	49.0	104.0
05	0.0	449.0	2.0	3.0
06	8.0	330.0	2.0	114.0
07	117.0	4.0	330.0	3.0
08	3.0	11.0	439.0	1.0
09	81.0	104.0	7.0	262.0
10	50.0	77.0	19.0	308.0
11	99.0	43.0	106.0	206.0
12	169.0	6.0	239.0	40.0
13	384.0	0.0	29.0	41.0
14	327.0	1.0	0.0	126.0
15	0.0	448.0	6.0	0.0
16	0.0	404.0	0.0	50.0
17	78.0	0.0	374.0	2.0
18	0.0	20.0	434.0	0.0
19	107.0	61.0	0.0	286.0
20	69.25	49.25	31.25	304.25
21	103.25	143.25	78.25	129.25

PFM

	A	C	G	T
01	0.267	0.269	0.209	0.256
02	0.39	0.144	0.355	0.111
03	0.674	0.031	0.15	0.145
04	0.65	0.013	0.108	0.229
05	0.0	0.989	0.004	0.007
06	0.018	0.727	0.004	0.251
07	0.258	0.009	0.727	0.007
08	0.007	0.024	0.967	0.002
09	0.178	0.229	0.015	0.577
10	0.11	0.17	0.042	0.678
11	0.218	0.095	0.233	0.454
12	0.372	0.013	0.526	0.088
13	0.846	0.0	0.064	0.09
14	0.72	0.002	0.0	0.278
15	0.0	0.987	0.013	0.0
16	0.0	0.89	0.0	0.11
17	0.172	0.0	0.824	0.004
18	0.0	0.044	0.956	0.0
19	0.236	0.134	0.0	0.63
20	0.153	0.108	0.069	0.67
21	0.227	0.316	0.172	0.285

PWM

	A	C	G	T
01	0.063	0.071	-0.175	0.022
02	0.441	-0.544	0.347	-0.798
03	0.983	-2.002	-0.503	-0.533
04	0.947	-2.726	-0.823	-0.086
05	-4.32	1.365	-3.484	-3.235
06	-2.491	1.059	-3.484	0.004
07	0.03	-3.035	1.059	-3.235
08	-3.235	-2.217	1.343	-3.817
09	-0.332	-0.086	-2.602	0.829
10	-0.803	-0.382	-1.723	0.99
11	-0.135	-0.949	-0.067	0.59
12	0.394	-2.726	0.738	-1.019
13	1.209	-4.32	-1.326	-0.995
14	1.049	-3.817	-4.32	0.103
15	-4.32	1.363	-2.726	-4.32
16	-4.32	1.26	-4.32	-0.803
17	-0.369	-4.32	1.183	-3.484
18	-4.32	-1.676	1.331	-4.32
19	-0.058	-0.61	-4.32	0.916
20	-0.486	-0.818	-1.255	0.978
21	-0.093	0.23	-0.366	0.128

Standard thresholds

P-value	Threshold
0.001	0.71941
0.0005	2.15526
0.0001	5.16541