CLOCK.H13INVITRO.0.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CLOCK.H13INVITRO.0.M.C
Gene (human)	CLOCK (GeneCards)
Gene synonyms (human)	BHLHE8, KIAA0334
Gene (mouse)	Clock
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	11
Consensus	nRCACATGTbn
GC content	47.53%
Information content (bits; total / per base)	12.352 / 1.123
Data sources	Methyl-HT-SELEX
Aligned words	9531
Previous names	CLOCK.H12INVITRO.0.M.C

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)	0.748	0.787	0.54	0.582	0.602	0.667	1.35	1.709	10.367	48.553
Mouse	10 (66)	0.768	0.828	0.568	0.624	0.674	0.698	1.622	1.772	39.586	71.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.855	0.827	0.811	0.792	0.783	0.77
Overall, 4 experiments	best	0.994	0.99	0.991	0.985	0.98	0.972
Methyl HT-SELEX, 1 experiments	median	0.994	0.99	0.991	0.985	0.98	0.972
Methyl HT-SELEX, 1 experiments	best	0.994	0.99	0.991	0.985	0.98	0.972
Non-Methyl HT-SELEX, 3 experiments	median	0.729	0.69	0.642	0.621	0.588	0.58
Non-Methyl HT-SELEX, 3 experiments	best	0.981	0.965	0.98	0.963	0.978	0.959

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.223	0.164	0.043	0.023

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.834	0.511	0.479	0.27
batch 2	0.807	0.627	0.374	0.242

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	CLOCK.H13INVITRO.0.M.C.pcm
PWM	CLOCK.H13INVITRO.0.M.C.pwm
PFM	CLOCK.H13INVITRO.0.M.C.pfm
Threshold to P-value map	CLOCK.H13INVITRO.0.M.C.thr
Motif in other formats
JASPAR format	CLOCK.H13INVITRO.0.M.C_jaspar_format.txt
MEME format	CLOCK.H13INVITRO.0.M.C_meme_format.meme
Transfac format	CLOCK.H13INVITRO.0.M.C_transfac_format.txt
Homer format	CLOCK.H13INVITRO.0.M.C_homer_format_0.001.txt CLOCK.H13INVITRO.0.M.C_homer_format_0.0005.txt CLOCK.H13INVITRO.0.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3004.0	1857.0	2536.0	2134.0
02	6352.0	1128.0	1884.0	167.0
03	239.0	9236.0	29.0	27.0
04	5794.0	4.0	3716.0	17.0
05	1.0	9518.0	0.0	12.0
06	8836.0	0.0	695.0	0.0
07	0.0	40.0	0.0	9491.0
08	1.0	1.0	9525.0	4.0
09	53.0	1464.0	431.0	7583.0
10	1261.25	2094.25	1654.25	4521.25
11	2352.75	2376.75	1636.75	3164.75

PFM

	A	C	G	T
01	0.315	0.195	0.266	0.224
02	0.666	0.118	0.198	0.018
03	0.025	0.969	0.003	0.003
04	0.608	0.0	0.39	0.002
05	0.0	0.999	0.0	0.001
06	0.927	0.0	0.073	0.0
07	0.0	0.004	0.0	0.996
08	0.0	0.0	0.999	0.0
09	0.006	0.154	0.045	0.796
10	0.132	0.22	0.174	0.474
11	0.247	0.249	0.172	0.332

PWM

	A	C	G	T
01	0.231	-0.249	0.062	-0.11
02	0.98	-0.747	-0.235	-2.645
03	-2.291	1.354	-4.334	-4.4
04	0.888	-5.938	0.444	-4.817
05	-6.586	1.384	-6.948	-5.117
06	1.31	-6.948	-1.23	-6.948
07	-6.948	-4.032	-6.948	1.381
08	-6.586	-6.586	1.385	-5.938
09	-3.764	-0.486	-1.706	1.157
10	-0.635	-0.129	-0.364	0.64
11	-0.013	-0.003	-0.375	0.284

Standard thresholds

P-value	Threshold
0.001	3.036315
0.0005	4.64687
0.0001	7.611385