CLOCK.H12INVITRO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CLOCK.H12INVITRO.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	nndMCACGTGYn
GC content	59.46%
Information content (bits; total / per base)	13.5 / 1.125
Data sources	ChIP-Seq + HT-SELEX
Aligned words	10000

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)	0.824	0.873	0.737	0.771	0.758	0.821	2.432	2.736	58.77	175.26
Mouse	10 (66)	0.855	0.92	0.733	0.823	0.772	0.881	2.429	3.347	109.502	174.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.84	0.827	0.789	0.774	0.753	0.74
Overall, 4 experiments	best	0.998	0.997	0.997	0.995	0.995	0.992
Methyl HT-SELEX, 1 experiments	median	0.977	0.962	0.958	0.935	0.935	0.908
Methyl HT-SELEX, 1 experiments	best	0.977	0.962	0.958	0.935	0.935	0.908
Non-Methyl HT-SELEX, 3 experiments	median	0.703	0.692	0.62	0.614	0.571	0.572
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
#	1.578	0.508	0.114	0.063

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.963	0.859	0.926	0.563
batch 2	0.88	0.826	0.831	0.6

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

PCM

	A	C	G	T
01	2826.0	2536.0	2410.0	2228.0
02	2858.75	1797.75	2255.75	3087.75
03	2295.0	910.0	5349.0	1446.0
04	4143.0	5312.0	537.0	8.0
05	24.0	9975.0	1.0	0.0
06	9992.0	0.0	4.0	4.0
07	1.0	9995.0	2.0	2.0
08	24.0	0.0	9976.0	0.0
09	1.0	19.0	1.0	9979.0
10	5.0	0.0	9879.0	116.0
11	228.75	4583.75	685.75	4501.75
12	2341.75	2966.75	2160.75	2530.75

PFM

	A	C	G	T
01	0.283	0.254	0.241	0.223
02	0.286	0.18	0.226	0.309
03	0.23	0.091	0.535	0.145
04	0.414	0.531	0.054	0.001
05	0.002	0.998	0.0	0.0
06	0.999	0.0	0.0	0.0
07	0.0	1.0	0.0	0.0
08	0.002	0.0	0.998	0.0
09	0.0	0.002	0.0	0.998
10	0.001	0.0	0.988	0.012
11	0.023	0.458	0.069	0.45
12	0.234	0.297	0.216	0.253

PWM

	A	C	G	T
01	0.122	0.014	-0.037	-0.115
02	0.134	-0.329	-0.103	0.211
03	-0.085	-1.009	0.76	-0.547
04	0.505	0.753	-1.535	-5.493
05	-4.555	1.383	-6.63	-6.991
06	1.385	-6.991	-5.984	-5.984
07	-6.63	1.385	-6.366	-6.366
08	-4.555	-6.991	1.383	-6.991
09	-6.63	-4.766	-6.63	1.384
10	-5.837	-6.991	1.373	-3.052
11	-2.382	0.606	-1.291	0.588
12	-0.065	0.171	-0.146	0.012

Standard thresholds

P-value	Threshold
0.001	1.415995
0.0005	2.65509
0.0001	7.062555