MYOD1.H13CORE.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MYOD1.H13CORE.1.PSM.A
Gene (human)	MYOD1 (GeneCards)
Gene synonyms (human)	BHLHC1, MYF3, MYOD
Gene (mouse)	Myod1
Gene synonyms (mouse)	Myod
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	10
Consensus	vCASCTGYYn
GC content	59.62%
Information content (bits; total / per base)	11.453 / 1.145
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	996
Previous names	MYOD1.H12CORE.1.PSM.A

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)	0.942	0.984	0.875	0.965	0.91	0.958	3.269	3.823	283.723	643.125
Mouse	31 (194)	0.946	0.979	0.892	0.949	0.91	0.95	3.26	3.71	348.834	538.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.921	0.893	0.83	0.803	0.722	0.715
Overall, 4 experiments	best	0.964	0.948	0.891	0.869	0.777	0.765
Methyl HT-SELEX, 2 experiments	median	0.844	0.806	0.735	0.71	0.644	0.639
Methyl HT-SELEX, 2 experiments	best	0.888	0.853	0.775	0.749	0.672	0.667
Non-Methyl HT-SELEX, 2 experiments	median	0.959	0.94	0.887	0.863	0.774	0.764
Non-Methyl HT-SELEX, 2 experiments	best	0.964	0.948	0.891	0.869	0.777	0.765

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.061	3.148	0.266	0.13

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.905	0.539	0.872	0.571

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.H13CORE.1.PSM.A.pcm
PWM	MYOD1.H13CORE.1.PSM.A.pwm
PFM	MYOD1.H13CORE.1.PSM.A.pfm
Threshold to P-value map	MYOD1.H13CORE.1.PSM.A.thr
Motif in other formats
JASPAR format	MYOD1.H13CORE.1.PSM.A_jaspar_format.txt
MEME format	MYOD1.H13CORE.1.PSM.A_meme_format.meme
Transfac format	MYOD1.H13CORE.1.PSM.A_transfac_format.txt
Homer format	MYOD1.H13CORE.1.PSM.A_homer_format_0.001.txt MYOD1.H13CORE.1.PSM.A_homer_format_0.0005.txt MYOD1.H13CORE.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	206.0	258.0	414.0	118.0
02	12.0	966.0	5.0	13.0
03	958.0	6.0	6.0	26.0
04	9.0	310.0	628.0	49.0
05	18.0	951.0	3.0	24.0
06	5.0	3.0	0.0	988.0
07	5.0	10.0	971.0	10.0
08	9.0	317.0	16.0	654.0
09	7.0	422.0	57.0	510.0
10	232.0	353.0	242.0	169.0

PFM

	A	C	G	T
01	0.207	0.259	0.416	0.118
02	0.012	0.97	0.005	0.013
03	0.962	0.006	0.006	0.026
04	0.009	0.311	0.631	0.049
05	0.018	0.955	0.003	0.024
06	0.005	0.003	0.0	0.992
07	0.005	0.01	0.975	0.01
08	0.009	0.318	0.016	0.657
09	0.007	0.424	0.057	0.512
10	0.233	0.354	0.243	0.17

PWM

	A	C	G	T
01	-0.188	0.035	0.506	-0.739
02	-2.905	1.351	-3.618	-2.835
03	1.342	-3.48	-3.48	-2.202
04	-3.152	0.218	0.921	-1.598
05	-2.542	1.335	-3.971	-2.277
06	-3.618	-3.971	-4.979	1.373
07	-3.618	-3.063	1.356	-3.063
08	-3.152	0.24	-2.649	0.961
09	-3.358	0.525	-1.451	0.713
10	-0.07	0.347	-0.028	-0.384

Standard thresholds

P-value	Threshold
0.001	4.304625
0.0005	5.058405
0.0001	7.710195