CLOCK.H12RSNP.0.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CLOCK.H12RSNP.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	13
Consensus	nnRCACATGTbhn
GC content	45.24%
Information content (bits; total / per base)	13.025 / 1.002
Data sources	Methyl-HT-SELEX
Aligned words	2434

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)	0.736	0.774	0.533	0.574	0.587	0.666	1.318	1.738	4.824	38.699
Mouse	10 (66)	0.754	0.816	0.554	0.61	0.662	0.689	1.62	1.767	33.427	57.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.853	0.826	0.808	0.79	0.781	0.768
Overall, 4 experiments	best	0.994	0.99	0.99	0.984	0.977	0.967
Methyl HT-SELEX, 1 experiments	median	0.994	0.99	0.99	0.984	0.977	0.967
Methyl HT-SELEX, 1 experiments	best	0.994	0.99	0.99	0.984	0.977	0.967
Non-Methyl HT-SELEX, 3 experiments	median	0.725	0.688	0.636	0.618	0.585	0.578
Non-Methyl HT-SELEX, 3 experiments	best	0.981	0.965	0.98	0.962	0.977	0.958

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	0.865	0.078	0.017	0.004

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.855	0.528	0.477	0.286
batch 2	0.818	0.61	0.376	0.259

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.H12RSNP.0.M.C.pcm
PWM	CLOCK.H12RSNP.0.M.C.pwm
PFM	CLOCK.H12RSNP.0.M.C.pfm
Alignment	CLOCK.H12RSNP.0.M.C.words.tsv
Threshold to P-value map	CLOCK.H12RSNP.0.M.C.thr
Motif in other formats
JASPAR format	CLOCK.H12RSNP.0.M.C_jaspar_format.txt
MEME format	CLOCK.H12RSNP.0.M.C_meme_format.meme
Transfac format	CLOCK.H12RSNP.0.M.C_transfac_format.txt
Homer format	CLOCK.H12RSNP.0.M.C_homer_format_0.001.txt CLOCK.H12RSNP.0.M.C_homer_format_0.0005.txt CLOCK.H12RSNP.0.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	835.5	391.5	549.5	657.5
02	847.75	435.75	630.75	519.75
03	1637.0	309.0	454.0	34.0
04	45.0	2379.0	4.0	6.0
05	1570.0	2.0	862.0	0.0
06	0.0	2421.0	0.0	13.0
07	2305.0	0.0	129.0	0.0
08	0.0	0.0	0.0	2434.0
09	1.0	0.0	2433.0	0.0
10	5.0	297.0	73.0	2059.0
11	217.0	462.0	384.0	1371.0
12	563.25	629.25	310.25	931.25
13	621.5	609.5	550.5	652.5

PFM

	A	C	G	T
01	0.343	0.161	0.226	0.27
02	0.348	0.179	0.259	0.214
03	0.673	0.127	0.187	0.014
04	0.018	0.977	0.002	0.002
05	0.645	0.001	0.354	0.0
06	0.0	0.995	0.0	0.005
07	0.947	0.0	0.053	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	1.0	0.0
10	0.002	0.122	0.03	0.846
11	0.089	0.19	0.158	0.563
12	0.231	0.259	0.127	0.383
13	0.255	0.25	0.226	0.268

PWM

	A	C	G	T
01	0.316	-0.439	-0.102	0.077
02	0.331	-0.333	0.036	-0.157
03	0.988	-0.675	-0.292	-2.832
04	-2.565	1.361	-4.631	-4.341
05	0.946	-5.041	0.347	-5.747
06	-5.747	1.379	-5.747	-3.71
07	1.329	-5.747	-1.539	-5.747
08	-5.747	-5.747	-5.747	1.384
09	-5.333	-5.747	1.383	-5.747
10	-4.476	-0.714	-2.097	1.217
11	-1.025	-0.274	-0.458	0.811
12	-0.077	0.033	-0.671	0.424
13	0.021	0.002	-0.1	0.07

Standard thresholds

P-value	Threshold
0.001	2.77816
0.0005	4.23016
0.0001	7.358275