MYOD1.H13RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MYOD1.H13RSNP.0.P.B
Gene (human)	MYOD1 (GeneCards)
Gene synonyms (human)	BHLHC1, MYF3, MYOD
Gene (mouse)	Myod1
Gene synonyms (mouse)	Myod
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	14
Consensus	CAGCTGYYbbbdbh
GC content	58.42%
Information content (bits; total / per base)	13.245 / 0.946
Data sources	ChIP-Seq
Aligned words	1001
Previous names	MYOD1.H12RSNP.0.P.B

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	12 (70)	0.944	0.978	0.876	0.938	0.918	0.96	3.585	4.252	286.245	601.569
Mouse	31 (194)	0.947	0.974	0.881	0.941	0.921	0.953	3.634	4.229	340.274	536.066

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.913	0.879	0.831	0.8	0.721	0.712
Overall, 4 experiments	best	0.954	0.933	0.884	0.856	0.781	0.763
Methyl HT-SELEX, 2 experiments	median	0.836	0.793	0.737	0.707	0.644	0.638
Methyl HT-SELEX, 2 experiments	best	0.879	0.839	0.779	0.747	0.676	0.667
Non-Methyl HT-SELEX, 2 experiments	median	0.951	0.927	0.883	0.854	0.773	0.76
Non-Methyl HT-SELEX, 2 experiments	best	0.954	0.933	0.884	0.856	0.781	0.763

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.122	4.287	0.361	0.172

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.92	0.598	0.874	0.548

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	MyoD-ASC-related {1.2.2} (TFClass)
TF subfamily	Myogenic TFs {1.2.2.1} (TFClass)
TFClass ID	TFClass: 1.2.2.1.1
HGNC	HGNC:7611
MGI	MGI:97275
EntrezGene (human)	GeneID:4654 (SSTAR profile)
EntrezGene (mouse)	GeneID:17927 (SSTAR profile)
UniProt ID (human)	MYOD1_HUMAN
UniProt ID (mouse)	MYOD1_MOUSE
UniProt AC (human)	P15172 (TFClass)
UniProt AC (mouse)	P10085 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	12 human, 31 mouse
HT-SELEX	2
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	MYOD1.H13RSNP.0.P.B.pcm
PWM	MYOD1.H13RSNP.0.P.B.pwm
PFM	MYOD1.H13RSNP.0.P.B.pfm
Threshold to P-value map	MYOD1.H13RSNP.0.P.B.thr
Motif in other formats
JASPAR format	MYOD1.H13RSNP.0.P.B_jaspar_format.txt
MEME format	MYOD1.H13RSNP.0.P.B_meme_format.meme
Transfac format	MYOD1.H13RSNP.0.P.B_transfac_format.txt
Homer format	MYOD1.H13RSNP.0.P.B_homer_format_0.001.txt MYOD1.H13RSNP.0.P.B_homer_format_0.0005.txt MYOD1.H13RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3.0	996.0	0.0	2.0
02	994.0	0.0	4.0	3.0
03	7.0	132.0	825.0	37.0
04	14.0	974.0	3.0	10.0
05	2.0	3.0	0.0	996.0
06	0.0	3.0	997.0	1.0
07	1.0	381.0	37.0	582.0
08	8.0	306.0	81.0	606.0
09	143.0	363.0	316.0	179.0
10	111.0	491.0	120.0	279.0
11	148.0	223.0	169.0	461.0
12	188.0	155.0	461.0	197.0
13	103.0	316.0	215.0	367.0
14	150.0	472.0	144.0	235.0

PFM

	A	C	G	T
01	0.003	0.995	0.0	0.002
02	0.993	0.0	0.004	0.003
03	0.007	0.132	0.824	0.037
04	0.014	0.973	0.003	0.01
05	0.002	0.003	0.0	0.995
06	0.0	0.003	0.996	0.001
07	0.001	0.381	0.037	0.581
08	0.008	0.306	0.081	0.605
09	0.143	0.363	0.316	0.179
10	0.111	0.491	0.12	0.279
11	0.148	0.223	0.169	0.461
12	0.188	0.155	0.461	0.197
13	0.103	0.316	0.215	0.367
14	0.15	0.472	0.144	0.235

PWM

	A	C	G	T
01	-3.976	1.376	-4.983	-4.214
02	1.374	-4.983	-3.784	-3.976
03	-3.363	-0.634	1.188	-1.873
04	-2.774	1.354	-3.976	-3.067
05	-4.214	-3.976	-4.983	1.376
06	-4.983	-3.976	1.377	-4.526
07	-4.526	0.418	-1.873	0.84
08	-3.254	0.2	-1.114	0.88
09	-0.554	0.37	0.232	-0.332
10	-0.804	0.671	-0.728	0.108
11	-0.521	-0.114	-0.389	0.608
12	-0.284	-0.475	0.608	-0.237
13	-0.878	0.232	-0.151	0.381
14	-0.507	0.631	-0.548	-0.062

Standard thresholds

P-value	Threshold
0.001	3.21556
0.0005	4.40071
0.0001	7.18616