MBD1.H14INVIVO.0.PSIB.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MBD1.H14INVIVO.0.PSIB.A
Gene (human)	MBD1 (GeneCards)
Gene synonyms (human)	CXXC3, PCM1
Gene (mouse)	Mbd1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	11
Consensus	nhKCGMYdhvn
GC content	55.84%
Information content (bits; total / per base)	6.837 / 0.622
Data sources	ChIP-Seq + HT-SELEX + SMiLe-Seq + PBM
Aligned words	694
Previous names

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	Centrality, median	Centrality, best
Overall	1 (1)	0.698	0.698	0.483	0.483	0.366	0.366	6.398	6.398

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
GFPIVT, 2 experiments	median	0.653	0.597	0.626	0.582	0.595	0.565
GFPIVT, 2 experiments	best	0.695	0.629	0.661	0.608	0.621	0.585

SMiLE-Seq benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 1 experiments	median	0.63	0.583	0.603	0.567	0.578	0.552
Overall, 1 experiments	best	0.63	0.583	0.603	0.567	0.578	0.552

PBM benchmarking		auROC, QNZS	auPR, QNZS	auROC, SD	auPR, SD
Overall, 3 experiments	median	0.696	0.009	0.635	0.017
Overall, 3 experiments	best	0.696	0.009	0.66	0.027

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	CXXC zinc finger factors {2.6} (TFClass)
TF family	CpG-binding {2.6.1} (TFClass)
TF subfamily	{2.6.1.0} (TFClass)
TFClass ID	TFClass: 2.6.1.0.2
HGNC	HGNC:6916
MGI	MGI:1333811
EntrezGene (human)	GeneID:4152 (SSTAR profile)
EntrezGene (mouse)	GeneID:17190 (SSTAR profile)
UniProt ID (human)	MBD1_HUMAN
UniProt ID (mouse)	MBD1_MOUSE
UniProt AC (human)	Q9UIS9 (TFClass)
UniProt AC (mouse)	Q9Z2E2 (TFClass)
GRECO-DB-TF	no

ChIP-Seq	1 human, 0 mouse
HT-SELEX	2 overall: 0 Lysate, 0 IVT, 2 GFPIVT
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	1
PBM	3

PCM	MBD1.H14INVIVO.0.PSIB.A.pcm
PWM	MBD1.H14INVIVO.0.PSIB.A.pwm
PFM	MBD1.H14INVIVO.0.PSIB.A.pfm
Threshold to P-value map	MBD1.H14INVIVO.0.PSIB.A.thr
Motif in other formats
JASPAR format	MBD1.H14INVIVO.0.PSIB.A_jaspar_format.txt
MEME format	MBD1.H14INVIVO.0.PSIB.A_meme_format.meme
Transfac format	MBD1.H14INVIVO.0.PSIB.A_transfac_format.txt
Homer format	MBD1.H14INVIVO.0.PSIB.A_homer_format_0.001.txt MBD1.H14INVIVO.0.PSIB.A_homer_format_0.0005.txt MBD1.H14INVIVO.0.PSIB.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	110.0	136.0	264.0	184.0
02	195.0	305.0	15.0	179.0
03	3.0	64.0	499.0	128.0
04	0.0	694.0	0.0	0.0
05	0.0	0.0	694.0	0.0
06	275.0	309.0	0.0	110.0
07	212.0	232.0	0.0	250.0
08	300.0	56.0	132.0	206.0
09	340.0	112.0	68.0	174.0
10	303.0	167.0	134.0	90.0
11	147.0	220.0	162.0	165.0

PFM

	A	C	G	T
01	0.159	0.196	0.38	0.265
02	0.281	0.439	0.022	0.258
03	0.004	0.092	0.719	0.184
04	0.0	1.0	0.0	0.0
05	0.0	0.0	1.0	0.0
06	0.396	0.445	0.0	0.159
07	0.305	0.334	0.0	0.36
08	0.432	0.081	0.19	0.297
09	0.49	0.161	0.098	0.251
10	0.437	0.241	0.193	0.13
11	0.212	0.317	0.233	0.238

PWM

	A	C	G	T
01	-0.45	-0.241	0.417	0.058
02	0.116	0.56	-2.354	0.031
03	-3.632	-0.981	1.05	-0.301
04	-4.674	1.379	-4.674	-4.674
05	-4.674	-4.674	1.379	-4.674
06	0.457	0.573	-4.674	-0.45
07	0.199	0.288	-4.674	0.362
08	0.544	-1.111	-0.27	0.17
09	0.668	-0.433	-0.922	0.003
10	0.554	-0.038	-0.256	-0.648
11	-0.164	0.235	-0.068	-0.05

Standard thresholds

P-value	Threshold
0.001	5.26587
0.0005	5.67618
0.0001	6.403125