MYOD1.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MYOD1.H12INVIVO.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	59.61%
Information content (bits; total / per base)	10.551 / 1.055
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	987

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	0.986	0.877	0.971	0.911	0.962	3.255	3.851	269.52	622.77
Mouse	31 (194)	0.945	0.979	0.893	0.954	0.908	0.951	3.27	3.766	339.766	526.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.912	0.884	0.808	0.785	0.707	0.7
Overall, 4 experiments	best	0.962	0.944	0.874	0.854	0.76	0.751
Methyl HT-SELEX, 2 experiments	median	0.829	0.794	0.714	0.694	0.631	0.628
Methyl HT-SELEX, 2 experiments	best	0.873	0.84	0.751	0.73	0.657	0.653
Non-Methyl HT-SELEX, 2 experiments	median	0.957	0.936	0.869	0.847	0.758	0.748
Non-Methyl HT-SELEX, 2 experiments	best	0.962	0.944	0.874	0.854	0.76	0.751

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.732	3.968	0.264	0.136

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.883	0.484	0.856	0.562

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

PCM	MYOD1.H12INVIVO.1.PSM.A.pcm
PWM	MYOD1.H12INVIVO.1.PSM.A.pwm
PFM	MYOD1.H12INVIVO.1.PSM.A.pfm
Alignment	MYOD1.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	MYOD1.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	MYOD1.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	MYOD1.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	MYOD1.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	MYOD1.H12INVIVO.1.PSM.A_homer_format_0.001.txt MYOD1.H12INVIVO.1.PSM.A_homer_format_0.0005.txt MYOD1.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	163.0	236.0	439.0	149.0
02	11.0	932.0	29.0	15.0
03	912.0	17.0	7.0	51.0
04	11.0	220.0	685.0	71.0
05	15.0	942.0	7.0	23.0
06	23.0	4.0	5.0	955.0
07	6.0	21.0	947.0	13.0
08	12.0	246.0	44.0	685.0
09	8.0	369.0	162.0	448.0
10	229.0	293.0	279.0	186.0

PFM

	A	C	G	T
01	0.165	0.239	0.445	0.151
02	0.011	0.944	0.029	0.015
03	0.924	0.017	0.007	0.052
04	0.011	0.223	0.694	0.072
05	0.015	0.954	0.007	0.023
06	0.023	0.004	0.005	0.968
07	0.006	0.021	0.959	0.013
08	0.012	0.249	0.045	0.694
09	0.008	0.374	0.164	0.454
10	0.232	0.297	0.283	0.188

PWM

	A	C	G	T
01	-0.411	-0.044	0.573	-0.5
02	-2.972	1.324	-2.09	-2.699
03	1.302	-2.586	-3.349	-1.55
04	-2.972	-0.114	1.017	-1.229
05	-2.699	1.334	-3.349	-2.308
06	-2.308	-3.771	-3.61	1.348
07	-3.471	-2.392	1.34	-2.826
08	-2.896	-0.003	-1.693	1.017
09	-3.241	0.4	-0.417	0.593
10	-0.074	0.171	0.122	-0.28

Standard thresholds

P-value	Threshold
0.001	4.594895
0.0005	5.32896
0.0001	7.63177