Transcriptional responses to ultraviolet and ionizing radiation: An approach based on graph curvature Conference Paper
| Authors: | Chen, Y.; Oh, J. H.; Sandhu, R.; Lee, S.; Deasy, J. O.; Tannenbaum, A. |
| Title: | Transcriptional responses to ultraviolet and ionizing radiation: An approach based on graph curvature |
| Conference Title: | 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) |
| 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 L1-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. © 2016 IEEE. |
| Keywords: | ultraviolet radiation; genes; gene expression; radiation; radiotherapy; reference database; radiation exposure; ionizing radiation; patient treatment; bioinformatics; radiation shielding; biological process; curve fitting; transcriptional response; gene expression levels; microarray dataset; treatment process; wasserstein distance |
| Journal Title | Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 |
| Conference Dates: | 2016 Dec 15-18 |
| Conference Location: | Shenzhen, China |
| ISBN: | 978-1-5090-1610-5 |
| Publisher: | Institute of Electrical and Electronics Engineers Inc. |
| Date Published: | 2016-01-01 |
| Start Page: | 1302 |
| End Page: | 1306 |
| Language: | English |
| DOI: | 10.1109/bibm.2016.7822706 |
| PROVIDER: | scopus |
| PMCID: | PMC5330782 |
| PUBMED: | 28261534 |
| DOI/URL: | |
| Notes: | Conference Paper -- Conference code: 125905 -- Export Date: 2 March 2017 -- Harbin Institute of Technology (HIT); IEEE; IEEE Computer Society; National Science Foundation (NSF) -- 15 December 2016 through 18 December 2016 -- Source: Scopus |
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