MYOD1.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MYOD1.H12INVIVO.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	15
Consensus	nCAGCTGYYbbbdbb
GC content	59.11%
Information content (bits; total / per base)	13.417 / 0.894
Data sources	ChIP-Seq
Aligned words	1000

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)	0.946	0.979	0.88	0.942	0.922	0.96	3.684	4.333	298.958	638.959
Mouse	31 (194)	0.95	0.976	0.891	0.945	0.924	0.956	3.719	4.254	356.703	566.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.916	0.884	0.829	0.801	0.72	0.712
Overall, 4 experiments	best	0.956	0.936	0.884	0.857	0.78	0.763
Methyl HT-SELEX, 2 experiments	median	0.839	0.797	0.737	0.708	0.646	0.639
Methyl HT-SELEX, 2 experiments	best	0.882	0.843	0.777	0.747	0.675	0.667
Non-Methyl HT-SELEX, 2 experiments	median	0.953	0.931	0.883	0.856	0.772	0.76
Non-Methyl HT-SELEX, 2 experiments	best	0.956	0.936	0.884	0.857	0.78	0.763

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.943	2.914	0.368	0.171

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.91	0.598	0.856	0.521

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.0.P.B.pcm
PWM	MYOD1.H12INVIVO.0.P.B.pwm
PFM	MYOD1.H12INVIVO.0.P.B.pfm
Alignment	MYOD1.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	MYOD1.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	MYOD1.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	MYOD1.H12INVIVO.0.P.B_meme_format.meme
Transfac format	MYOD1.H12INVIVO.0.P.B_transfac_format.txt
Homer format	MYOD1.H12INVIVO.0.P.B_homer_format_0.001.txt MYOD1.H12INVIVO.0.P.B_homer_format_0.0005.txt MYOD1.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	233.0	233.0	425.0	109.0
02	2.0	996.0	0.0	2.0
03	990.0	1.0	3.0	6.0
04	6.0	155.0	814.0	25.0
05	8.0	981.0	3.0	8.0
06	4.0	2.0	0.0	994.0
07	0.0	2.0	998.0	0.0
08	0.0	359.0	35.0	606.0
09	5.0	306.0	68.0	621.0
10	128.0	338.0	349.0	185.0
11	97.0	486.0	128.0	289.0
12	151.0	230.0	192.0	427.0
13	204.0	148.0	433.0	215.0
14	106.0	312.0	243.0	339.0
15	171.0	452.0	174.0	203.0

PFM

	A	C	G	T
01	0.233	0.233	0.425	0.109
02	0.002	0.996	0.0	0.002
03	0.99	0.001	0.003	0.006
04	0.006	0.155	0.814	0.025
05	0.008	0.981	0.003	0.008
06	0.004	0.002	0.0	0.994
07	0.0	0.002	0.998	0.0
08	0.0	0.359	0.035	0.606
09	0.005	0.306	0.068	0.621
10	0.128	0.338	0.349	0.185
11	0.097	0.486	0.128	0.289
12	0.151	0.23	0.192	0.427
13	0.204	0.148	0.433	0.215
14	0.106	0.312	0.243	0.339
15	0.171	0.452	0.174	0.203

PWM

	A	C	G	T
01	-0.07	-0.07	0.528	-0.821
02	-4.213	1.377	-4.982	-4.213
03	1.371	-4.525	-3.975	-3.484
04	-3.484	-0.474	1.176	-2.243
05	-3.253	1.362	-3.975	-3.253
06	-3.783	-4.213	-4.982	1.375
07	-4.982	-4.213	1.379	-4.982
08	-4.982	0.36	-1.925	0.881
09	-3.622	0.201	-1.284	0.906
10	-0.663	0.3	0.332	-0.299
11	-0.936	0.661	-0.663	0.144
12	-0.5	-0.083	-0.262	0.532
13	-0.202	-0.52	0.546	-0.15
14	-0.849	0.22	-0.028	0.303
15	-0.377	0.589	-0.359	-0.207

Standard thresholds

P-value	Threshold
0.001	3.10286
0.0005	4.27491
0.0001	7.13086