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Functional & Integrative Genomics

, Volume 17, Issue 1, pp 53–68 | Cite as

Analysis of the interplay between methylation and expression reveals its potential role in cancer aetiology

  • Bugra Ozer
  • Ugur Sezerman
Original Article

Abstract

With ongoing developments in technology, changes in DNA methylation levels have become prevalent to study cancer biology. Previous studies report that DNA methylation affects gene expression in a direct manner, most probably by blocking gene regulatory regions. In this study, we have studied the interplay between methylation and expression to improve our knowledge of cancer aetiology. For this purpose, we have investigated which genomic regions are of higher importance; hence, first exon, 5′UTR and 200 bp near the transcription start sites are proposed as being more crucial compared to other genomic regions. Furthermore, we have searched for a valid methylation level change threshold, and as a result, 25 % methylation change in previously determined genomic regions showed the highest inverse correlation with expression data. As a final step, we have examined the commonly affected genes and pathways by integrating methylation and expression information. Remarkably, the GPR115 gene and ErbB signalling pathway were found to be significantly altered for all cancer types in our analysis. Overall, combining methylation and expression information and identifying commonly affected genes and pathways in a variety of cancer types revealed new insights of cancer disease mechanisms. Moreover, compared to previous methylation-based studies, we have identified more important genomic regions and have defined a methylation change threshold level in order to obtain more reliable results. In addition to the novel analysis framework that involves the analysis of four different cancer types, our study exposes essential information regarding the contribution of methylation changes and its impact on cancer disease biology, which may facilitate the identification of new drug targets.

Keywords

Bioinformatics Methylation Expression Data integration Integrative analysis Functional enrichment analysis Cancer biology 

Notes

Acknowledgments

We would like to thank the National Cancer Institute for The Cancer Genome Atlas (TCGA) for making essential cancer data from different platforms publicly available.

Authors’ contributions

BO and US wrote the article together. US was the advisor in the whole procedure. BO performed all analyses including DNA methylation and RNA-Seq expression analysis. Both authors have read and approved the manuscript for publication.

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.

Supplementary material

10142_2016_533_MOESM1_ESM.docx (16 kb)
ESM 1 Additional file 1—45 genes that are shared by at least 3 types of cancers with more than 25 % methylation change. List of significantly methylated genes (FDR < 0.05) for thyroid, breast, colon and prostate cancers. Only the genes that are shared by more than two cancer types are shown at this table. In addition, descriptions associated with each gene are also added to table using Genecards suite. (DOCX 16 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Advanced Genomics and Bioinformatics Research Center (IGBAM)The Scientific and Technological Research Council of Turkey (TUBITAK)GebzeTurkey
  2. 2.Department of Biostatistics and Medical InformaticsAcibadem UniversityIstanbulTurkey
  3. 3.Biological Sciences and Bioengineering ProgramFaculty of Engineering and Natural Sciences, Sabanci UniversityIstanbulTurkey

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