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. 2020 Jan 1:2020:baaa045.
doi: 10.1093/database/baaa045.

Curation of cancer hallmark-based genes and pathways for in silico characterization of chemical carcinogenesis

Peir-In Liang  1   2 , Chia-Chi Wang  3 , Hsien-Jen Cheng  4 , Shan-Shan Wang  5 , Ying-Chi Lin  1   6 , Pinpin Lin  4 , Chun-Wei Tung  4   5
Affiliations

Curation of cancer hallmark-based genes and pathways for in silico characterization of chemical carcinogenesis

Peir-In Liang et al. Database (Oxford). .

Abstract

Exposure to toxic substances in the environment is one of the most important causes of cancer. However, the time-consuming process for the identification and characterization of carcinogens is not applicable to a huge amount of testing chemicals. The data gaps make the carcinogenic risk uncontrollable. An efficient and effective way of prioritizing chemicals of carcinogenic concern with interpretable mechanism information is highly desirable. This study presents a curation work for genes and pathways associated with 11 hallmarks of cancer (HOCs) reported by the Halifax Project. To demonstrate the usefulness of the curated HOC data, the interacting HOC genes and affected HOC pathways of chemicals of the three carcinogen lists from IARC, NTP and EPA were analyzed using the in silico toxicogenomics ChemDIS system. Results showed that a higher number of affected HOCs were observed for known carcinogens than the other chemicals. The curated HOC data is expected to be useful for prioritizing chemicals of carcinogenic concern. Database URL: The HOC database is available at https://github.com/hocdb-KMU-TMU/hocdb and the website of Database journal as Supplementary Data.

Keywords: cancer hallmark; curation; the Halifax Project.

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Figures

Figure 1
Figure 1
System flow of the curation work for hallmarks of cancer.
Figure 2
Figure 2
The number of affected hallmarks of cancer (HOCs) for different groups of IARC chemicals. IARC, international agency for research on cancer; G1, IARC Group 1 chemicals; G2A, IARC Group 2A chemicals; G2B, IARC Group 2B chemicals; G3, IARC Group 3 chemicals; G4, IARC Group 4 chemicals.
Figure 3
Figure 3
The number of affected hallmarks of cancer (HOCs) for different groups of National Toxicology Program chemicals. NTP, National Toxicology Program; KHC, known to be a human carcinogen; RAHC, reasonably anticipated to be a human carcinogen.
Figure 4
Figure 4
The number of affected hallmarks of cancer (HOCs) for different groups of Environmental Protection Agency chemicals. EPA, Environmental Protection Agency; A, Group A chemicals after regroup chemicals classes that previously classified based on the EPA guidelines published in 1986 or 2005; B, Group B; C, Group C; D, Group D; E, Group E.
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