CLARE: Cracking the LAnguage of Regulatory Elements

Request ID...
example
perm link: https://clare.dcode.org/?id=example

Characteristics of the positive set
average element length: 1250.08 bps
average GC content: 41.6 %
[A: 0.283%, G: 0.205%, C: 0.196%, T: 0.279%]

De novo predicted motifs (PRIORITY)



click to enlarge matrices for de novo motifs

Descriptive features

	motif	weight
1.	V$WT1_Q6	1009.55
2.	V$AP2_Q6	664.94
3.	V$MINI19_B	583.48
4.	V$AP4_Q6_01	467.4
5.	V$J3_NFYA_	432.29
6.	V$CHCH_01	390.39
7.	V$UF1H3BETA_Q6	355.74
8.	V$MYOD_Q6_01	348.31
9.	V$WHN_B	330.86
10.	V$AP2ALPHA_01	220.66
11.	V$E2F_Q2	216.5
12.	V$LBP1_Q6	162.79
13.	V$PAX8_B	157.38
14.	V$AR_Q6	147.57
15.	V$RBPJK_01	139.79
16.	V$RFX1_02	137.71
17.	V$LEF1_Q2_01	117.19
18.	V$PAX4_03	111.94
19.	V$SOX17_01	99.68
20.	V$E2F1_Q3_01	99.25
21.	V$OCT1_03	90.92
22.	V$J3_RORA_1_HSAP	90.81
23.	V$IPF1_Q4	87.44
24.	V$J3_BAPX1_MMUS	86.88
25.	V$SPZ1_01	84.64
26.	V$TAL1BETAE47_01	76.76
27.	V$CRX_Q4	73.21
28.	V$OCT1_B	71.12
29.	V$GATA1_03	63.77
30.	V$MEIS1_01	60.74
31.	V$J3_SOX9_HSAP	55.61
32.	V$GFI1B_01	51.25
33.	V$OCT1_04	41.27
34.	V$ELF1_Q6	38.69
35.	V$J3_MYF_HSAP	36.63
36.	V$E2F_Q6_01	35.2
37.	V$ZIC2_01	31.89
38.	V$OCT_Q6	30.88
39.	V$PXRRXR_02	26.46
40.	V$OCT4_01	22.84
41.	9_PRIORITY	21.26
42.	V$PAX6_01	20.77
43.	V$MOVOB_01	14.88
44.	V$J3_LHX3_MMUS	13.3
45.	V$POU1F1_Q6	10.86
46.	V$MEF2_01	8.82
47.	V$PTF1BETA_Q6	8.61
48.	V$LMAF_Q2	7.99
49.	V$NANOG_01	7.12
50.	V$CEBP_Q2	6.74
51.	V$NKX25_02	6.53
52.	4_PRIORITY	6.31
53.	V$GEN_INI2_B	5.28
54.	V$ZIC3_01	5.01
55.	V$J3_T_MMUS	2.66
56.	V$PXR_Q2	-0.85
57.	V$ATATA_B	-1.47
58.	V$NFKAPPAB65_01	-3
59.	V$MYB_Q5_01	-3.15
60.	V$FOXO3A_Q1	-5.71
61.	V$TEF_Q6	-8.63
62.	V$AR_02	-9.5
63.	V$TAACC_B	-10.52
64.	V$ETS_Q4	-10.97
65.	V$AP2ALPHA_03	-11.01
66.	V$FAC1_01	-13.63
67.	V$HNF4ALPHA_Q6	-13.79
68.	V$SEF1_C	-14.83
69.	V$J3_TCF11-MAFG_GGAL	-16.71
70.	V$CDP_02	-18.38
71.	V$TEL2_Q6	-21.53
72.	V$FXR_IR1_Q6	-24.47
73.	V$COUP_01	-25.18
74.	V$PEA3_Q6	-25.21
75.	V$P53_01	-26.58
76.	V$GATA_C	-26.61
77.	V$TCF11MAFG_01	-30.6
78.	V$PR_01	-36
79.	V$J3_MYC-MAX_HSAP	-37.91
80.	V$PADS_C	-39.09
81.	V$PU1_Q6	-39.39
82.	V$HTF_01	-43.62
83.	V$IRF2_01	-43.71
84.	V$AREB6_02	-46.82
85.	V$ELK1_01	-48.62
86.	V$MYB_Q3	-50.77
87.	V$J3_GATA3_HSAP	-52.86
88.	V$STAT5B_01	-59.29
89.	V$LMO2COM_02	-59.79
90.	V$STAT6_02	-69.61
91.	V$GR_01	-71.65
92.	V$NFKB_Q6	-73.74
93.	V$XBP1_01	-82.01
94.	V$AIRE_02	-86.34
95.	V$USF_Q6_01	-96.24
96.	V$GATA3_03	-100.12
97.	V$CETS1P54_02	-100.91
98.	V$J3_ZNF354_HSAP	-103.13
99.	V$PPARA_01	-110.85
100.	V$SP1_Q6	-111.03
101.	V$STAT5A_01	-119.84
102.	V$CDXA_01	-121.11
103.	V$TBX5_02	-121.53
104.	V$MUSCLE_INI_B	-134.46
105.	V$GR_Q6_01	-135.15
106.	V$J3_REST_HSAP	-144.11
107.	V$TITF1_Q3	-157.19
108.	V$CREB_Q2_01	-169.13
109.	V$LFA1_Q6	-180.39
110.	V$USF_C	-241.95
111.	V$J3_ROAZ_RNOR	-765.1
...

Full list of descriptive features with weights

click to enlarge

Motifs in the signal set

Distribution of motifs in the signal set	Motif densities in the training data
click on image to see detailed reports

Model accuracy

Area under the ROC curve (AUC): 0.83

Operating point:
TPR: 0.26
FPR: 0.05

click to enlarge

Locus scan

Sliding window: length = 150 bp, step = 75 bp

3168 positively scoring elements have been found
12.87% of 24623 examined sliding windows have been scored positively

List of positively scoring elements

click to enlarge

Raw input/output data...

	49 signal sequences	list
	147 background (control) sequences	list
	LARS training	output
	Scanned locus	sequence

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{ Cracking the LAnguage of Regulatory Elements }