Identifying novel oncogenes: A machine learning approach

Abstract

Genome sequencing has overflowed the databases with huge amount of SNP data. Although the amount of detected single nucleotide polymorphisms (SNPs) is rising exponentially every day, we still lag behind in characterization techniques. Implementing computational platforms to determine the pathogenecity associated with the SNPs can provide a probable solution to this problem. To improve the prediction quality for SNP characterization methods, we implemented machine learning support vector classification method. Total 557 non-synonymous amino acid variants were collected from CENP family proteins, excluding CENPE. Multivariate simulation of associated changes in biological phenomena's for each SNPs was computed through available SNP analysis platforms. Support vector model was designed using training dataset and the raw classification data was subjected to the classification hyperplane. We observed multiple evidences of cancer associated genetic mutations in CENPI, CENPJ, CENPK, CENPL and CENPX protein. The former four proteins have showed positive hits in cosmic database for mutations in tumour samples, but CENPX has never been reported before for the cancer associated outcomes. Since CENPX has been recently classified and not much functional and pathological insight has been, the results obtained in this study will serve as a starting point for future investigation on cancer research in association to CENPX protein.

FAM172A expression in circulating tumor cells for prediction of high-risk subgroups of colorectal cancer

“…Most of these studies focus on the correlation of CTC enumeration with prognosis 9–13. However, recent studies showed that only enumerated CTCs were not enough to reflect the heterogeneous condition of tumors 3,14,15.…”

CENPL, ISG20L2, LSM4 , MRPL3 Are Four Novel Hub Genes and May Serve as Diagnostic and Prognostic Markers in Breast Cancer

“…Further exploration of their correlations with clinicopathological variables as well as their diagnostic and prognostic values were conducted. Centromere Protein L (CENPL) is a component of the CENPA-CAD (nucleosome distal) complex, which participated in the assembly process of kinetochore proteins, mitotic progression and chromosome segregation 26 . Interferon stimulated exonuclease gene 20 Like 2 (ISG20L2) encodes a 3'-5' exoribonuclease that involved in the 12S pre-rRNA processing, as a target gene of miR-139-3p, has been reported to take part in the pathogenesis of hepatocellular carcinoma 27,28 .…”

CENPL, ISG20L2, LSM4 and MRPL3 Are Four Novel Hub Genes Involved in Breast Cancer Development and Progression

“…Centromere Protein L (CENPL) is a component of the CENPA-CAD (nucleosome distal) complex, which participated in the assembly process of kinetochore proteins, mitotic progression and chromosome segregation [57]. Interferon Stimulated Exonuclease Gene 20 Like 2 (ISG20L2) encodes a 3'-5' exoribonuclease that involved in the 12S pre-rRNA processing, as a target gene of miR-139-3p, has been reported to take part in the pathogenesis of hepatocellular carcinoma [58,59].…”