In the quest to unravel the intricate mechanisms underlying tumors, understanding cancer is crucial for developing effective treatments. The Cancer-Alterome project addresses this challenge by presenting a literature-mined dataset focusing on the regulatory events within an organism's biological processes or clinical phenotypes induced by genetic alterations.
CancerAlterome aims to construct a comprehensive data resource for the Regulatory Events caused by Genetic Alteration (GARE) in the context of cancer. The project defines two categories of gene alterations: gene/protein single nucleotide polymorphisms (SNPs) or point mutations captured by LitVar, and other genetic alterations described in the literature by AGAC corpus, such as gene expression changes and epigenetic modifications. Meanwhile, the downstream biological process is described and normalized using the Gene Ontology (GO) and Human Phenotype Ontology (HPO) in CancerAlterome, facilitating rapid investigation by users. The complete definition of regulatory events is based on the previously developed AGAC corpus.
The complete Cancer-Alterome pipeline construction and data visualization implementation can be accessed on our GitHub repository.
[1] Yao, X., He, Z., Liu, Y. et al. Cancer-Alterome: a literature-mined resource for regulatory events caused by genetic alterations in cancer. Sci Data 11, 265 (2024). https://doi.org/10.1038/s41597-024-03083-9
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Author:Xinzhi Yao Email:xinzhi_bioinfo@163.com
PI of HZAU BioNLP-Lab:Jingbo Xia Email:Xiajingbo.math@gmail.com
Affiliation: China, Hubei, Wuhan, Huazhong Agricultural University, Collega of Informatics