Background: The analysis of cancer diversity based on a logical framework of hallmarks has greatly improved our understanding of the occurrence, development and metastasis of various cancers.
Methods: We designed Cancer Hallmark Genes (CHG) database which focuses on integrating hallmark genes in a systematic, standard way and annotates the potential roles of the hallmark genes in cancer processes. Following the conceptual criteria description of hallmark function the keywords for each hallmark were manually selected from the literature. Candidate hallmark genes collected were derived from 301 pathways of KEGG database by Lucene and manually corrected.
Results: Based on the variation data, we finally identified the hallmark genes of various types of cancer and constructed CHG. And we also analyzed the relationships among hallmarks and potential characteristics and relationships of hallmark genes based on the topological structures of their networks. We manually confirm the hallmark gene identified by CHG based on literature and database. We also predicted the prognosis of breast cancer, glioblastoma multiforme and kidney papillary cell carcinoma patients based on CHG data.
Conclusions: In summary, CHG, which was constructed based on a hallmark feature set, provides a new perspective for analyzing the diversity and development of cancers.
Keywords: Hallmark genes; annotating Hallmark features; copy number variation; database; methylation; mutation.
Copyright © 2020 Zhang, Huo, Xie, Wu, Zhang, Liu, Jin and Chen.