MYOD1.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MYOD1.H12RSNP.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	13
Consensus	RWCAGCTGTTvhn
GC content	49.5%
Information content (bits; total / per base)	16.112 / 1.239
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	307

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)	0.902	0.948	0.81	0.877	0.842	0.91	2.829	3.342	199.314	425.721
Mouse	31 (194)	0.895	0.945	0.8	0.877	0.844	0.893	2.775	3.151	244.593	348.398

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.939	0.922	0.832	0.818	0.708	0.713
Overall, 4 experiments	best	0.975	0.966	0.889	0.871	0.764	0.761
Methyl HT-SELEX, 2 experiments	median	0.854	0.832	0.731	0.719	0.634	0.639
Methyl HT-SELEX, 2 experiments	best	0.909	0.889	0.779	0.765	0.663	0.671
Non-Methyl HT-SELEX, 2 experiments	median	0.972	0.961	0.887	0.871	0.758	0.759
Non-Methyl HT-SELEX, 2 experiments	best	0.975	0.966	0.889	0.871	0.764	0.761

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.285	3.476	0.223	0.122

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.934	0.668	0.908	0.617

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.H12RSNP.1.PSM.A.pcm
PWM	MYOD1.H12RSNP.1.PSM.A.pwm
PFM	MYOD1.H12RSNP.1.PSM.A.pfm
Alignment	MYOD1.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	MYOD1.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	MYOD1.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	MYOD1.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	MYOD1.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	MYOD1.H12RSNP.1.PSM.A_homer_format_0.001.txt MYOD1.H12RSNP.1.PSM.A_homer_format_0.0005.txt MYOD1.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	158.25	26.25	108.25	14.25
02	239.0	17.0	17.0	34.0
03	0.0	300.0	0.0	7.0
04	301.0	6.0	0.0	0.0
05	0.0	49.0	254.0	4.0
06	3.0	298.0	0.0	6.0
07	0.0	0.0	0.0	307.0
08	0.0	1.0	306.0	0.0
09	0.0	8.0	0.0	299.0
10	0.0	17.0	0.0	290.0
11	111.0	121.0	55.0	20.0
12	57.0	147.0	44.0	59.0
13	46.0	93.0	108.0	60.0

PFM

	A	C	G	T
01	0.515	0.086	0.353	0.046
02	0.779	0.055	0.055	0.111
03	0.0	0.977	0.0	0.023
04	0.98	0.02	0.0	0.0
05	0.0	0.16	0.827	0.013
06	0.01	0.971	0.0	0.02
07	0.0	0.0	0.0	1.0
08	0.0	0.003	0.997	0.0
09	0.0	0.026	0.0	0.974
10	0.0	0.055	0.0	0.945
11	0.362	0.394	0.179	0.065
12	0.186	0.479	0.143	0.192
13	0.15	0.303	0.352	0.195

PWM

	A	C	G	T
01	0.714	-1.038	0.339	-1.607
02	1.123	-1.445	-1.445	-0.791
03	-4.0	1.35	-4.0	-2.227
04	1.353	-2.353	-4.0	-4.0
05	-4.0	-0.438	1.184	-2.667
06	-2.87	1.343	-4.0	-2.353
07	-4.0	-4.0	-4.0	1.372
08	-4.0	-3.47	1.369	-4.0
09	-4.0	-2.115	-4.0	1.346
10	-4.0	-1.445	-4.0	1.316
11	0.363	0.449	-0.326	-1.294
12	-0.291	0.641	-0.543	-0.258
13	-0.5	0.189	0.336	-0.241

Standard thresholds

P-value	Threshold
0.001	2.23141
0.0005	3.552265
0.0001	6.29881