title: Transcriptional Responses to Ultraviolet and Ionizing Radiation: An Approach Based on Graph Curvature.
abstract: More than half of all cancer patients receive radiotherapy in their treatment process. However, our understanding of abnormal transcriptional responses to radiation remains poor. In this study, we employ an extended definition of Ollivier-Ricci curvature based on LI-Wasserstein distance to investigate genes and biological processes associated with ionizing radiation (IR) and ultraviolet radiation (UV) exposure using a microarray dataset. Gene expression levels were modeled on a gene interaction topology downloaded from the Human Protein Reference Database (HPRD). This was performed for IR, UV, and mock datasets, separately. The difference curvature value between IR and mock graphs (also between UV and mock) for each gene was used as a metric to estimate the extent to which the gene responds to radiation. We found that in comparison of the top 200 genes identified from IR and UV graphs, about 20~30% genes were overlapping. Through gene ontology enrichment analysis, we found that the metabolic-related biological process was highly associated with both IR and UV radiation exposure.
authors.affiliation: Department of Medical Physics, Memorial Sloan Kettering Cancer Center, NY, USA.
authors.forename: Yongxin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Medical Physics, Memorial Sloan Kettering Cancer Center, NY, USA.
authors.forename: Jung Hun
authors.initials: JH
authors.lastname: Oh
authors.affiliation: Department of Biomedical Informatics, Stony Brook University, NY, USA.
authors.forename: Romeil
authors.initials: R
authors.lastname: Sandhu
authors.affiliation: Department of Medical Physics, Memorial Sloan Kettering Cancer Center, NY, USA.
authors.forename: Sangkyu
authors.initials: S
authors.lastname: Lee
authors.affiliation: Department of Medical Physics, Memorial Sloan Kettering Cancer Center, NY, USA.
authors.forename: Joseph O
authors.initials: JO
authors.lastname: Deasy
authors.affiliation: Department of Computer Science and Applied Mathematics & Statistics, Stony Brook University, NY, USA.
authors.forename: Allen
authors.initials: A
authors.lastname: Tannenbaum