SCRT1.H14INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SCRT1.H14INVIVO.0.PSM.A
Gene (human)	SCRT1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Scrt1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	14
Consensus	ddKCAACAGGTKbn
GC content	49.17%
Information content (bits; total / per base)	16.445 / 1.175
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1001
Previous names	SCRT1.H12INVIVO.0.PSM.A

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	2 (12)	0.963	0.994	0.938	0.991	0.949	0.988	4.514	6.471	324.918	824.469

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.829	0.841	0.787	0.796	0.769	0.776
Overall, 4 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	1.0	0.999	0.999	0.998
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	1.0	0.999	0.999	0.998
Non-Methyl HT-SELEX, 3 experiments	median	0.658	0.681	0.573	0.592	0.54	0.554
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	1.0	1.0	0.999

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.987	0.753	0.95	0.648
batch 2	0.922	0.815	0.914	0.659

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	More than 3 adjacent zinc fingers {2.3.3} (TFClass)
TF subfamily	Snail-like {2.3.3.2} (TFClass)
TFClass ID	TFClass: 2.3.3.2.4
HGNC	HGNC:15950
MGI	MGI:2176606
EntrezGene (human)	GeneID:83482 (SSTAR profile)
EntrezGene (mouse)	GeneID:170729 (SSTAR profile)
UniProt ID (human)	SCRT1_HUMAN
UniProt ID (mouse)	SCRT1_MOUSE
UniProt AC (human)	Q9BWW7 (TFClass)
UniProt AC (mouse)	Q99M85 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 0 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	SCRT1.H14INVIVO.0.PSM.A.pcm
PWM	SCRT1.H14INVIVO.0.PSM.A.pwm
PFM	SCRT1.H14INVIVO.0.PSM.A.pfm
Threshold to P-value map	SCRT1.H14INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	SCRT1.H14INVIVO.0.PSM.A_jaspar_format.txt
MEME format	SCRT1.H14INVIVO.0.PSM.A_meme_format.meme
Transfac format	SCRT1.H14INVIVO.0.PSM.A_transfac_format.txt
Homer format	SCRT1.H14INVIVO.0.PSM.A_homer_format_0.001.txt SCRT1.H14INVIVO.0.PSM.A_homer_format_0.0005.txt SCRT1.H14INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	568.0	100.0	217.0	116.0
02	317.0	93.0	112.0	479.0
03	4.25	36.25	433.25	527.25
04	0.25	986.25	2.25	12.25
05	898.25	67.25	17.25	18.25
06	988.25	0.25	8.25	4.25
07	0.25	1000.25	0.25	0.25
08	993.25	0.25	0.25	7.25
09	117.25	4.25	877.25	2.25
10	6.25	3.25	980.25	11.25
11	4.25	19.25	2.25	975.25
12	89.25	69.25	710.25	132.25
13	141.25	184.25	413.25	262.25
14	143.25	344.25	208.25	305.25

PFM

	A	C	G	T
01	0.567	0.1	0.217	0.116
02	0.317	0.093	0.112	0.479
03	0.004	0.036	0.433	0.527
04	0.0	0.985	0.002	0.012
05	0.897	0.067	0.017	0.018
06	0.987	0.0	0.008	0.004
07	0.0	0.999	0.0	0.0
08	0.992	0.0	0.0	0.007
09	0.117	0.004	0.876	0.002
10	0.006	0.003	0.979	0.011
11	0.004	0.019	0.002	0.974
12	0.089	0.069	0.71	0.132
13	0.141	0.184	0.413	0.262
14	0.143	0.344	0.208	0.305

PWM

	A	C	G	T
01	0.816	-0.907	-0.142	-0.761
02	0.235	-0.978	-0.796	0.646
03	-3.741	-1.892	0.546	0.742
04	-4.848	1.366	-4.149	-2.892
05	1.273	-1.296	-2.586	-2.535
06	1.368	-4.848	-3.229	-3.741
07	-4.848	1.38	-4.848	-4.848
08	1.373	-4.848	-4.848	-3.335
09	-0.75	-3.741	1.249	-4.149
10	-3.453	-3.924	1.36	-2.966
11	-3.741	-2.486	-4.149	1.355
12	-1.019	-1.267	1.039	-0.632
13	-0.567	-0.304	0.499	0.047
14	-0.553	0.317	-0.182	0.197

Standard thresholds

P-value	Threshold
0.001	1.47826
0.0005	2.89356
0.0001	5.88721