MYOD1.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MYOD1.H12INVITRO.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	CAGCTGYYbbbbbb
GC content	59.33%
Information content (bits; total / per base)	13.191 / 0.942
Data sources	ChIP-Seq
Aligned words	999

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)	0.943	0.977	0.877	0.935	0.919	0.959	3.613	4.226	298.608	614.432
Mouse	31 (194)	0.946	0.974	0.884	0.941	0.921	0.951	3.673	4.256	344.208	560.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.915	0.882	0.834	0.804	0.719	0.713
Overall, 4 experiments	best	0.954	0.934	0.888	0.859	0.777	0.762
Methyl HT-SELEX, 2 experiments	median	0.84	0.796	0.742	0.711	0.644	0.639
Methyl HT-SELEX, 2 experiments	best	0.882	0.841	0.784	0.751	0.675	0.668
Non-Methyl HT-SELEX, 2 experiments	median	0.951	0.928	0.886	0.857	0.771	0.76
Non-Methyl HT-SELEX, 2 experiments	best	0.954	0.934	0.888	0.859	0.777	0.762

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.448	3.677	0.362	0.172

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.914	0.575	0.866	0.551

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.H12INVITRO.0.P.B.pcm
PWM	MYOD1.H12INVITRO.0.P.B.pwm
PFM	MYOD1.H12INVITRO.0.P.B.pfm
Alignment	MYOD1.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	MYOD1.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	MYOD1.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	MYOD1.H12INVITRO.0.P.B_meme_format.meme
Transfac format	MYOD1.H12INVITRO.0.P.B_transfac_format.txt
Homer format	MYOD1.H12INVITRO.0.P.B_homer_format_0.001.txt MYOD1.H12INVITRO.0.P.B_homer_format_0.0005.txt MYOD1.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1.0	997.0	1.0	0.0
02	999.0	0.0	0.0	0.0
03	5.0	216.0	755.0	23.0
04	14.0	971.0	6.0	8.0
05	2.0	1.0	1.0	995.0
06	0.0	2.0	994.0	3.0
07	1.0	360.0	37.0	601.0
08	8.0	318.0	83.0	590.0
09	147.0	342.0	320.0	190.0
10	110.0	516.0	111.0	262.0
11	161.0	223.0	180.0	435.0
12	127.0	210.0	449.0	213.0
13	104.0	289.0	243.0	363.0
14	123.0	477.0	196.0	203.0

PFM

	A	C	G	T
01	0.001	0.998	0.001	0.0
02	1.0	0.0	0.0	0.0
03	0.005	0.216	0.756	0.023
04	0.014	0.972	0.006	0.008
05	0.002	0.001	0.001	0.996
06	0.0	0.002	0.995	0.003
07	0.001	0.36	0.037	0.602
08	0.008	0.318	0.083	0.591
09	0.147	0.342	0.32	0.19
10	0.11	0.517	0.111	0.262
11	0.161	0.223	0.18	0.435
12	0.127	0.21	0.449	0.213
13	0.104	0.289	0.243	0.363
14	0.123	0.477	0.196	0.203

PWM

	A	C	G	T
01	-4.524	1.379	-4.524	-4.981
02	1.381	-4.981	-4.981	-4.981
03	-3.621	-0.144	1.102	-2.319
04	-2.772	1.353	-3.483	-3.252
05	-4.212	-4.524	-4.524	1.377
06	-4.981	-4.212	1.376	-3.974
07	-4.524	0.364	-1.871	0.874
08	-3.252	0.24	-1.088	0.856
09	-0.525	0.312	0.246	-0.271
10	-0.811	0.722	-0.802	0.048
11	-0.435	-0.112	-0.325	0.552
12	-0.67	-0.172	0.584	-0.158
13	-0.866	0.145	-0.027	0.372
14	-0.701	0.644	-0.24	-0.206

Standard thresholds

P-value	Threshold
0.001	3.13916
0.0005	4.30721
0.0001	7.295265