QSAR Study for Carcinogenic Potency of Aromatic Amines Based on GEP and MLPs
Abstract
:1. Introduction
2. Methodology
2.1. Source of AA Data
2.2. Calculation of Molecular Descriptors
2.3. Theory of Gene Expression Programming
- If GEP_Rule (X) > 0 Then X ∈ class A
- ELSE X ∈ class B
- X stands for properties of instance.
2.4. Multilayer Perceptrons (MLPs)
2.5. Platform of Weka
3. Results and Discussion
3.1. Significance of the Descriptors
3.2. Results of GEP
3.3. The Results of MLPs
3.4. Comparison between GEP and MLPs
4. Conclusions
Author Contributions
Conflicts of Interest
References
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No. | Aromatic Amines | Carcinogenicity (exp) | Carcinogenicity (GEP) | Carcinogenicity (MLPs) |
---|---|---|---|---|
1 | N-Acetoxy-4-biphenylacetamide | 0 | 0 | 0 |
2 | N-Acetoxy-2-fluorenylacetamide | 0 | 0 | 0 |
3 | N-Acetoxy-4-phenanthrylacetamide | 0 | 0 | 0 |
4 | N-Acetoxy-N-(4-stilbenyl)acetamide | 0 | 0 | 0 |
5 | 3-Amino-s-triazole | 1 | 1 | 1 |
6 | 1-Anthramine | 0 | 0 | 0 |
7 | 9-Anthramine | 0 | 0 | 0 |
8 | 2-Anthranilacetamide | 0 | 0 | 0 |
9 | Benzidine | 1 | 0 | 1 |
10 | N-(Benzoyloxy)-fluorenylacetamide | 0 | 1 | 0 |
11 | 4-Biphenyldimethylamine | 0 | 0 | 0 |
12 | 3,6-Bis(dimethylamino)acridine | 1 | 0 | 1 |
13 | 2-Chloro-4-phenylaniline | 0 | 1 | 0 |
14 | 4′-Chloro-4-stilbenyl-N,N-dimethylamine | 0 | 0 | 0 |
15 | 2-Cyano-4-stilbenamine | 1 | 0 | 0 |
16 | 4,6-Diamino-2-(5-nitro-2-furyl)-s-triazine | 0 | 1 | 1 |
17 | 0,0′-Dianisidine | 0 | 0 | 0 |
18 | 3-Dibenzofuranylacetamide | 0 | 0 | 0 |
19 | 3-Dibenzothiophenylacetamide | 0 | 0 | 0 |
20 | 2,2′-Dichloro-4,4′-diaminostilbene | 1 | 0 | 1 |
21 | 3,3′-Dichloro-4,4′-diaminostilbene | 0 | 1 | 0 |
22 | 9,10-Dihydro-2-phenanthramine | 0 | 0 | 0 |
23 | 3,3′-Dihydroxybenzidine | 0 | 0 | 0 |
24 | 2-(4-(N,N-Dimethylamino)styryl) quinoline | 0 | 0 | 0 |
25 | 3,2′-Dimethyl-4-biphenylamine | 0 | 0 | 0 |
26 | 3,3′-Dimethyl-4-biphenylamine | 0 | 0 | 0 |
27 | 2-Fluorenylacetamide | 1 | 0 | 0 |
28 | 3-Fluorenylacetamide | 0 | 0 | 0 |
29 | 1-Fluorenylaceto hydroxamic acid | 0 | 0 | 0 |
30 | 2-Fluorenylaceto hydroxanic acid | 1 | 0 | 0 |
31 | N-Fluorenyl-2-benzamide | 0 | 1 | 0 |
32 | N-Fluorenyl-2-benzohydroxamic acid | 0 | 0 | 0 |
33 | 2-Fluorenyldiacetamide | 1 | 0 | 1 |
34 | 2-Fluorenyldimethylamine | 1 | 1 | 1 |
35 | 2,5-Fluorenylenediacetamide | 0 | 0 | 0 |
36 | 2-Fluorenylhydroxylamine | 0 | 0 | 0 |
37 | N-(2-Fluorenyl)-2,2,2-trifluoroacetamide | 1 | 0 | 1 |
38 | 4′-Fluoro-4-biphenylamine | 1 | 0 | 1 |
39 | 1-Fluoro-2-fluorenylacetamide | 0 | 0 | 1 |
40 | 3-Fluoro-2-fluorenylacetamide | 1 | 0 | 0 |
41 | 4-Fluoro-2-fluorenylacetamide | 0 | 0 | 0 |
42 | 5-Fluoro-2-fluorenylacetamide | 0 | 1 | 0 |
43 | 6-Fluoro-2-fluorenylacetamide | 1 | 0 | 0 |
44 | 7-Fluoro-2-fluorenylacetamide | 1 | 0 | 0 |
45 | 7-Fluoro-2-N-fluorenylacetohydroxamic acid | 1 | 1 | 0 |
46 | 4′-Fluoro-p-phenylaniline | 0 | 1 | 0 |
47 | 4′-Fluoro-4-stilbenamine | 1 | 1 | 0 |
48 | 4′-Fluoro-4-stilbenyl-N,N-dimethylamine | 1 | 0 | 0 |
49 | 2-Hydrazino-4-phenylthiazole | 0 | 1 | 0 |
50 | N-Hydroxy-N-(4-stilbenyl) acetamide | 0 | 1 | 0 |
51 | 3-Iodo-2-fluorenylacetamide | 0 | 0 | 0 |
52 | 7-Iodo-2-fluroenylacetamide | 0 | 0 | 0 |
53 | 2-Methoxy-3-benzofuranylamine | 0 | 0 | 0 |
54 | 7-Methoxy-2-fluorenylacetamide | 1 | 0 | 1 |
55 | 1-Methoxy-2-fluorenylamine | 1 | 0 | 1 |
56 | 3-Methoxy-2-fluorenylamine | 0 | 1 | 0 |
57 | 4-((p-Methoxyphenyl)azo)-o-anisidine | 1 | 0 | 1 |
58 | 2-Methyldiacetylbenzidine | 0 | 0 | 1 |
59 | 4,4′-Methylenebis(2-chloroaniline) | 1 | 1 | 1 |
60 | 4′-Methyl-4-phenylacetanilide | 0 | 0 | 0 |
61 | 3-Methyl-4-phenylaniline | 0 | 1 | 0 |
62 | 3-Methyl-4-stilbenamine | 0 | 0 | 0 |
63 | 1-Naphthylacetohydroxamic acid | 0 | 0 | 0 |
64 | 2-Naphthylhydroxylamine | 0 | 0 | 0 |
65 | 9-Oxo-2-fluorenylacetamide | 1 | 0 | 0 |
66 | 1-Phenanthrylacetamide | 0 | 0 | 0 |
67 | 2-Phenanthrylacetamide | 0 | 1 | 0 |
68 | 1-Phenanthrylamine | 0 | 0 | 0 |
69 | 3-Phenanthrylamine | 0 | 0 | 0 |
70 | 9-Phenanthrylamine | 0 | 0 | 0 |
71 | 4-(Phenylazo) acetanilide | 0 | 0 | 0 |
72 | 4-(Phenylazo) aniline | 0 | 0 | 0 |
73 | 4-(Phenylazo) diacetanilide | 0 | 0 | 0 |
74 | 4-(Phenylazo)-N-phenylacetohydroxamic acid | 0 | 0 | 0 |
75 | 4-Stilbenamine | 0 | 0 | 0 |
76 | N-(4-Stilbenyl) acetamide | 0 | 0 | 0 |
77 | 4-Stilbenyl-N,N-diethylamine | 0 | 0 | 0 |
78 | 4-Stilbenyl-N,N-dimethylamine | 0 | 0 | 0 |
79 | N-(4-Styrylphenyl) hydroxylamine | 0 | 0 | 0 |
80 | 3,2′,4′,6′-Tetramethyl-4-biphenylamine | 1 | 0 | 0 |
81 | o,o′-Tolidine | 0 | 1 | 0 |
82 | 4-(m-Tolylazo) acetanilide | 0 | 0 | 0 |
83 | 4-(m-Tolylazo) aniline | 0 | 0 | 0 |
84 | 2-(o-Tolylazo)-p-toluidine | 1 | 0 | 1 |
85 | 2-(p-Tolylazo)-p-toluidine | 0 | 0 | 0 |
86 | 4-(o-Tolylazo)-o-toluidine | 1 | 1 | 0 |
87 | 4-(o-Tolylazo)-m-toluidine | 0 | 0 | 0 |
88 | 4-(m-Tolylazo)-m-toluidine | 0 | 0 | 0 |
89 | 4-(p-Tolylazo)-o-toluidine | 0 | 0 | 0 |
90 | 4-(p-Tolylazo)-m-toluidine | 0 | 0 | 0 |
91 | N,N,2′-Trimethyl-4-stilbenamine | 0 | 0 | 0 |
92 | N,N,3′-Trimethyl-4-stilbenamine | 0 | 0 | 0 |
93 | N,N,4′-Trimethyl-4-stilbenamine | 0 | 0 | 0 |
No. | Aromatic Amines | Carcinogenicity (exp) | Carcinogenicity (GEP) | Carcinogenicity (MLPs) |
---|---|---|---|---|
1 | 2-Anthramine | 0 | 0 | 0 |
2 | 4-Biphenylacetamide | 0 | 0 | 0 |
3 | 4-Biphenylacetohydroxamic acid | 0 | 1 | 0 |
4 | 3-Carbazolylacetamide | 0 | 0 | 1 |
5 | 2,7-Diaminofluorene | 0 | 0 | 1 |
6 | 4,4′-Diaminostilbene | 1 | 1 | 0 |
7 | 2-Dibenzothiophenylacetamide | 0 | 0 | 0 |
8 | 3,3′-Dichlorobenzidine | 0 | 0 | 0 |
9 | 2-Fluorenamine | 1 | 1 | 0 |
10 | 1-Fluorenylacetamide | 0 | 0 | 0 |
11 | 3-Fluorenylaceto hydroxanic acid | 0 | 0 | 0 |
12 | 2,7-Fluorenyldiacetamide | 1 | 1 | 0 |
13 | 2-Fluorenyldiethylamine | 0 | 0 | 0 |
14 | N,2-Fluorenylformamide | 0 | 1 | 0 |
15 | 2-Fluorenylmethylamine | 1 | 0 | 0 |
16 | N,2-Fluorenylsuccinamic acid | 1 | 0 | 0 |
17 | 8-Fluoro-2-fluorenylacetamide | 1 | 0 | 1 |
18 | 2-Fluoro-4-phenylaniline | 0 | 0 | 0 |
19 | 3′-Fluoro-4-phenylaniline | 0 | 0 | 0 |
20 | 3-Methoxy-4-biphenylamine | 0 | 1 | 1 |
21 | 3-Methoxy-2-fluorenylacetamide | 0 | 1 | 0 |
22 | 4,4′-Methylenebis(2-methylaniline) | 1 | 0 | 1 |
23 | 3-Methyl-2-naphthylamine | 0 | 0 | 0 |
24 | 2-Methyl-4-phenylaniline | 0 | 0 | 0 |
25 | 2′-Methyl-4-phenylaniline | 0 | 0 | 0 |
26 | 2-Methyl-4-stilbenamine | 0 | 1 | 0 |
27 | 2-Naphthylamine | 0 | 0 | 0 |
28 | 1-Naphthylhydroxylamine | 0 | 0 | 0 |
29 | 9-Phenanthrylacetamide | 0 | 0 | 0 |
30 | 2-Phenanthrylacetohydroxamic acid | 0 | 0 | 0 |
31 | 2-Phenanthrylamine | 0 | 1 | 0 |
32 | 4-(Phynylazo)-o-anisidine | 1 | 1 | 0 |
33 | 1-(Phenylazo)-2-naphthylamine | 0 | 0 | 0 |
34 | 4-(Phenylazo)-N-phenylhydroxylamine | 0 | 0 | 0 |
35 | 3,2′,5′-Trimethyl-4-diphenylamine | 1 | 0 | 1 |
Correlation | NCOS | NNOS | KFBI | BBI | SICI | TEIA | PLPT | LUMO |
---|---|---|---|---|---|---|---|---|
NCOS | 1.000 | −0.227 | 0.649 | −0.708 | 0.667 | 0.234 | −0.034 | −0.374 |
NNOS | 1.000 | 0.175 | −0.014 | 0.159 | 0.312 | −0.201 | −0.111 | |
KFBI | 1.000 | −0.569 | 0.730 | 0.433 | 0.007 | −0.18 | ||
BBI | 1.000 | −0.681 | −0.259 | −0.173 | 0.438 | |||
SICI | 1.000 | 0.620 | 0.250 | −0.456 | ||||
TEIA | 1.000 | 0.339 | −0.107 | |||||
PLPT | 1.000 | −0.277 | ||||||
LUMO | 1.000 |
Accuracy | Sensitivity | Specificity | Youden’s Index | |
---|---|---|---|---|
Training set of GEP | 0.914 | 0.947 | 0.905 | 0.852 |
Test set of GEP | 0.829 | 0.667 | 0.885 | 0.552 |
Training set of MLPS | 0.838 | 0.844 | 0.813 | 0.657 |
Test set of MLPS | 0.743 | 0.793 | 0.500 | 0.293 |
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Song, F.; Zhang, A.; Liang, H.; Cui, L.; Li, W.; Si, H.; Duan, Y.; Zhai, H. QSAR Study for Carcinogenic Potency of Aromatic Amines Based on GEP and MLPs. Int. J. Environ. Res. Public Health 2016, 13, 1141. https://doi.org/10.3390/ijerph13111141
Song F, Zhang A, Liang H, Cui L, Li W, Si H, Duan Y, Zhai H. QSAR Study for Carcinogenic Potency of Aromatic Amines Based on GEP and MLPs. International Journal of Environmental Research and Public Health. 2016; 13(11):1141. https://doi.org/10.3390/ijerph13111141
Chicago/Turabian StyleSong, Fucheng, Anling Zhang, Hui Liang, Lianhua Cui, Wenlian Li, Hongzong Si, Yunbo Duan, and Honglin Zhai. 2016. "QSAR Study for Carcinogenic Potency of Aromatic Amines Based on GEP and MLPs" International Journal of Environmental Research and Public Health 13, no. 11: 1141. https://doi.org/10.3390/ijerph13111141