CLOCK.H12INVIVO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CLOCK.H12INVIVO.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	13
Consensus	nnvKCACGTGKvn
GC content	61.05%
Information content (bits; total / per base)	10.936 / 0.841
Data sources	ChIP-Seq + HT-SELEX
Aligned words	998

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)	0.844	0.902	0.775	0.851	0.816	0.885	3.149	3.769	74.658	208.509
Mouse	10 (66)	0.892	0.933	0.8	0.889	0.85	0.926	2.961	3.888	152.808	228.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.826	0.792	0.782	0.758	0.743	0.724
Overall, 4 experiments	best	0.992	0.984	0.991	0.983	0.99	0.981
Methyl HT-SELEX, 1 experiments	median	0.954	0.912	0.951	0.912	0.92	0.882
Methyl HT-SELEX, 1 experiments	best	0.954	0.912	0.951	0.912	0.92	0.882
Non-Methyl HT-SELEX, 3 experiments	median	0.698	0.673	0.613	0.603	0.566	0.565
Non-Methyl HT-SELEX, 3 experiments	best	0.992	0.984	0.991	0.983	0.99	0.981

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.636	3.411	0.15	0.071

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.904	0.575	0.889	0.578
batch 2	0.807	0.653	0.782	0.554

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.H12INVIVO.1.PS.A.pcm
PWM	CLOCK.H12INVIVO.1.PS.A.pwm
PFM	CLOCK.H12INVIVO.1.PS.A.pfm
Alignment	CLOCK.H12INVIVO.1.PS.A.words.tsv
Threshold to P-value map	CLOCK.H12INVIVO.1.PS.A.thr
Motif in other formats
JASPAR format	CLOCK.H12INVIVO.1.PS.A_jaspar_format.txt
MEME format	CLOCK.H12INVIVO.1.PS.A_meme_format.meme
Transfac format	CLOCK.H12INVIVO.1.PS.A_transfac_format.txt
Homer format	CLOCK.H12INVIVO.1.PS.A_homer_format_0.001.txt CLOCK.H12INVIVO.1.PS.A_homer_format_0.0005.txt CLOCK.H12INVIVO.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	192.0	351.0	278.0	177.0
02	264.0	227.0	326.0	181.0
03	228.0	256.0	388.0	126.0
04	124.0	10.0	403.0	461.0
05	7.0	985.0	4.0	2.0
06	971.0	5.0	8.0	14.0
07	1.0	973.0	12.0	12.0
08	188.0	27.0	777.0	6.0
09	34.0	54.0	24.0	886.0
10	2.0	0.0	923.0	73.0
11	6.0	171.0	547.0	274.0
12	214.0	481.0	165.0	138.0
13	221.0	336.0	189.0	252.0

PFM

	A	C	G	T
01	0.192	0.352	0.279	0.177
02	0.265	0.227	0.327	0.181
03	0.228	0.257	0.389	0.126
04	0.124	0.01	0.404	0.462
05	0.007	0.987	0.004	0.002
06	0.973	0.005	0.008	0.014
07	0.001	0.975	0.012	0.012
08	0.188	0.027	0.779	0.006
09	0.034	0.054	0.024	0.888
10	0.002	0.0	0.925	0.073
11	0.006	0.171	0.548	0.275
12	0.214	0.482	0.165	0.138
13	0.221	0.337	0.189	0.253

PWM

	A	C	G	T
01	-0.26	0.339	0.107	-0.34
02	0.056	-0.094	0.266	-0.318
03	-0.089	0.026	0.439	-0.676
04	-0.692	-3.065	0.477	0.611
05	-3.36	1.368	-3.781	-4.211
06	1.354	-3.62	-3.252	-2.771
07	-4.523	1.356	-2.907	-2.907
08	-0.281	-2.169	1.131	-3.482
09	-1.95	-1.506	-2.279	1.262
10	-4.211	-4.98	1.303	-1.213
11	-3.482	-0.375	0.781	0.093
12	-0.152	0.653	-0.41	-0.587
13	-0.12	0.296	-0.276	0.01

Standard thresholds

P-value	Threshold
0.001	4.43846
0.0005	5.383615
0.0001	7.58476