CLOCK.H12CORE.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CLOCK.H12CORE.1.PS.A
Gene (human)	CLOCK (GeneCards)
Gene synonyms (human)	BHLHE8, KIAA0334
Gene (mouse)	Clock
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	12
Consensus	ddvCACGTGTWh
GC content	49.04%
Information content (bits; total / per base)	15.196 / 1.266
Data sources	ChIP-Seq + HT-SELEX
Aligned words	631

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	3 (17)	0.761	0.803	0.692	0.737	0.695	0.746	2.101	2.573	39.215	126.921
Mouse	10 (66)	0.718	0.856	0.636	0.779	0.728	0.818	2.217	2.819	75.998	125.071

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.835	0.824	0.787	0.773	0.746	0.734
Overall, 4 experiments	best	0.998	0.997	0.997	0.995	0.995	0.992
Methyl HT-SELEX, 1 experiments	median	0.979	0.967	0.96	0.941	0.926	0.901
Methyl HT-SELEX, 1 experiments	best	0.979	0.967	0.96	0.941	0.926	0.901
Non-Methyl HT-SELEX, 3 experiments	median	0.692	0.68	0.613	0.606	0.566	0.567
Non-Methyl HT-SELEX, 3 experiments	best	0.998	0.997	0.997	0.995	0.995	0.992

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.459	0.388	0.118	0.054

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.949	0.859	0.958	0.62
batch 2	0.874	0.835	0.84	0.574

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	PAS {1.2.5} (TFClass)
TF subfamily	PAS-ARNT {1.2.5.2} (TFClass)
TFClass ID	TFClass: 1.2.5.2.5
HGNC	HGNC:2082
MGI	MGI:99698
EntrezGene (human)	GeneID:9575 (SSTAR profile)
EntrezGene (mouse)	GeneID:12753 (SSTAR profile)
UniProt ID (human)	CLOCK_HUMAN
UniProt ID (mouse)	CLOCK_MOUSE
UniProt AC (human)	O15516 (TFClass)
UniProt AC (mouse)	O08785 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 10 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	CLOCK.H12CORE.1.PS.A.pcm
PWM	CLOCK.H12CORE.1.PS.A.pwm
PFM	CLOCK.H12CORE.1.PS.A.pfm
Alignment	CLOCK.H12CORE.1.PS.A.words.tsv
Threshold to P-value map	CLOCK.H12CORE.1.PS.A.thr
Motif in other formats
JASPAR format	CLOCK.H12CORE.1.PS.A_jaspar_format.txt
MEME format	CLOCK.H12CORE.1.PS.A_meme_format.meme
Transfac format	CLOCK.H12CORE.1.PS.A_transfac_format.txt
Homer format	CLOCK.H12CORE.1.PS.A_homer_format_0.001.txt CLOCK.H12CORE.1.PS.A_homer_format_0.0005.txt CLOCK.H12CORE.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	171.25	85.25	106.25	268.25
02	91.0	64.0	290.0	186.0
03	286.0	179.0	135.0	31.0
04	0.0	631.0	0.0	0.0
05	631.0	0.0	0.0	0.0
06	0.0	631.0	0.0	0.0
07	0.0	0.0	631.0	0.0
08	0.0	0.0	0.0	631.0
09	0.0	0.0	631.0	0.0
10	0.0	2.0	10.0	619.0
11	117.0	66.0	30.0	418.0
12	162.25	128.25	93.25	247.25

PFM

	A	C	G	T
01	0.271	0.135	0.168	0.425
02	0.144	0.101	0.46	0.295
03	0.453	0.284	0.214	0.049
04	0.0	1.0	0.0	0.0
05	1.0	0.0	0.0	0.0
06	0.0	1.0	0.0	0.0
07	0.0	0.0	1.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	1.0	0.0
10	0.0	0.003	0.016	0.981
11	0.185	0.105	0.048	0.662
12	0.257	0.203	0.148	0.392

PWM

	A	C	G	T
01	0.081	-0.607	-0.39	0.527
02	-0.543	-0.887	0.604	0.163
03	0.59	0.125	-0.154	-1.587
04	-4.594	1.379	-4.594	-4.594
05	1.379	-4.594	-4.594	-4.594
06	-4.594	1.379	-4.594	-4.594
07	-4.594	-4.594	1.379	-4.594
08	-4.594	-4.594	-4.594	1.379
09	-4.594	-4.594	1.379	-4.594
10	-4.594	-3.787	-2.619	1.36
11	-0.295	-0.857	-1.618	0.968
12	0.028	-0.205	-0.519	0.446

Standard thresholds

P-value	Threshold
0.001	1.85209
0.0005	3.38681
0.0001	5.654815