A SVM Model for Candidate Y-chromosome Gene Discovery in Prostate Cancer

10 pages•Published: March 18, 2019

Wageesha Rasanjana, Sandun Rajapaksa, Indika Perera and Dulani Meedeniya

Abstract

Prostate cancer is widely known to be one of the most common cancers among men around the world. Due to its high heterogeneity, many of the studies carried out to identify the molecular level causes for cancer have only been partially successful. Among the techniques used in cancer studies, gene expression profiling is seen to be one of the most popular techniques due to its high usage. Gene expression profiles reveal information about the functionality of genes in different body tissues at different conditions. In order to identify cancer-decisive genes, differential gene expression analysis is carried out using statistical and machine learning methodologies. It helps to extract information about genes that have significant expression differences between healthy tissues and cancerous tissues. In this paper, we discuss a comprehensive supervised classification approach using Support Vector Machine (SVM) models to investigate differentially expressed Y-chromosome genes in prostate cancer. 8 SVM models, which are tuned to have 98.3% average accuracy have been used for the analysis. We were able to capture genes like CD99 (MIC2), ASMTL, DDX3Y and TXLNGY to come out as the best candidates. Some of our results support existing findings while introducing novel findings to be possible prostate cancer candidates.

Keyphrases: differential expression, log fold change, microarray data, prostate cancer, support vector machines, y chromosome

In: Oliver Eulenstein, Hisham Al-Mubaid and Qin Ding (editors). Proceedings of 11th International Conference on Bioinformatics and Computational Biology, vol 60, pages 129-138.

Links:	https://easychair.org/publications/paper/nV39
	https://doi.org/10.29007/3nzw

BibTeX entry

@inproceedings{BiCOB2019:SVM_Model_Candidate_Y,
  author    = {Wageesha Rasanjana and Sandun Rajapaksa and Indika Perera and Dulani Meedeniya},
  title     = {A SVM Model for Candidate Y-chromosome Gene Discovery in Prostate Cancer},
  booktitle = {Proceedings of 11th International Conference on Bioinformatics and Computational Biology},
  editor    = {Oliver Eulenstein and Hisham Al-Mubaid and Qin Ding},
  series    = {EPiC Series in Computing},
  volume    = {60},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2398-7340},
  url       = {/publications/paper/nV39},
  doi       = {10.29007/3nzw},
  pages     = {129-138},
  year      = {2019}}

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