MYOD1.H12INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MYOD1.H12INVITRO.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	11
Consensus	vvCAvCTGTTn
GC content	50.5%
Information content (bits; total / per base)	11.841 / 1.076
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	7721

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)	0.9	0.948	0.808	0.881	0.852	0.909	2.812	3.208	211.155	452.495
Mouse	31 (194)	0.897	0.945	0.797	0.876	0.853	0.898	2.777	3.138	272.6	395.131

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.959	0.944	0.868	0.853	0.742	0.744
Overall, 4 experiments	best	0.983	0.975	0.926	0.909	0.804	0.8
Methyl HT-SELEX, 2 experiments	median	0.887	0.864	0.766	0.751	0.662	0.664
Methyl HT-SELEX, 2 experiments	best	0.939	0.92	0.818	0.803	0.696	0.7
Non-Methyl HT-SELEX, 2 experiments	median	0.981	0.971	0.922	0.906	0.796	0.794
Non-Methyl HT-SELEX, 2 experiments	best	0.983	0.975	0.926	0.909	0.804	0.8

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.068	3.176	0.177	0.096

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.954	0.722	0.852	0.554

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.1.PSM.A.pcm
PWM	MYOD1.H12INVITRO.1.PSM.A.pwm
PFM	MYOD1.H12INVITRO.1.PSM.A.pfm
Alignment	MYOD1.H12INVITRO.1.PSM.A.words.tsv
Threshold to P-value map	MYOD1.H12INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	MYOD1.H12INVITRO.1.PSM.A_jaspar_format.txt
MEME format	MYOD1.H12INVITRO.1.PSM.A_meme_format.meme
Transfac format	MYOD1.H12INVITRO.1.PSM.A_transfac_format.txt
Homer format	MYOD1.H12INVITRO.1.PSM.A_homer_format_0.001.txt MYOD1.H12INVITRO.1.PSM.A_homer_format_0.0005.txt MYOD1.H12INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2881.25	1414.25	2883.25	542.25
02	3299.75	1434.75	2085.75	900.75
03	105.0	7267.0	111.0	238.0
04	7090.0	109.0	373.0	149.0
05	1017.0	2618.0	3159.0	927.0
06	931.0	6677.0	113.0	0.0
07	0.0	0.0	0.0	7721.0
08	0.0	0.0	7719.0	2.0
09	151.0	215.0	11.0	7344.0
10	11.0	2008.0	44.0	5658.0
11	2131.75	2408.75	2239.75	940.75

PFM

	A	C	G	T
01	0.373	0.183	0.373	0.07
02	0.427	0.186	0.27	0.117
03	0.014	0.941	0.014	0.031
04	0.918	0.014	0.048	0.019
05	0.132	0.339	0.409	0.12
06	0.121	0.865	0.015	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.02	0.028	0.001	0.951
10	0.001	0.26	0.006	0.733
11	0.276	0.312	0.29	0.122

PWM

	A	C	G	T
01	0.4	-0.311	0.401	-1.267
02	0.536	-0.296	0.077	-0.761
03	-2.892	1.325	-2.837	-2.085
04	1.3	-2.855	-1.639	-2.548
05	-0.64	0.304	0.492	-0.732
06	-0.728	1.24	-2.82	-6.761
07	-6.761	-6.761	-6.761	1.385
08	-6.761	-6.761	1.385	-6.122
09	-2.535	-2.186	-4.983	1.335
10	-4.983	0.039	-3.733	1.075
11	0.099	0.221	0.149	-0.718

Standard thresholds

P-value	Threshold
0.001	3.99659
0.0005	5.1241
0.0001	7.474005