Bilkent University
Department of Computer Engineering


The Effect of Dissecting out Proliferation from Cancer


Dr. Eren Kavak
Genomize, CEO

The pathological trajectory leading to transformed cells capable of creating tumors in vivo has been intensively studied at the transcriptome level. Recently, a general shortening of the 3' untranslated region was observed in transformed cells, indicative of cancer-associated alterations of the regulatory capacity of mRNAs. Here, we performed comprehensive analyses of 3' UTR expressions in cancer and normal cells and tissues, to address whether 3' UTR shortening is associated with the transformed cellular state in vivo. To distinguish transformation effects from proliferation effects, we developed an analyses method that adjusts for changes in proliferation between cells or samples. Surprisingly, we observed that most cancers showed no global shortening in 3' UTRs, and that no gene was found to have consistent shortening of 3' UTR across the panel of cancers studied. In fact, only a small minority of cancers exhibited significant 3' UTR shortening (or lengthening), demonstrating that 3' UTR regulation is cancer type-specific. Finally, we provide initial evidence that proliferation-adjusted cancer gene expression analyses can uncovered gene sets associated with many hallmarks of cancer that are obscured by the dominant signature of proliferation in normal gene expression analyses.

Bio: Eren is a scientist and entrepreneur specialized on genome-wide production and analysis of high throughput data. He was graduated from Bogazici University Genetics Department and had a PhD in molecular biology. He worked at Karolinksa Institute for 7 years during and after completing his PhD on big data integration with microarray and sequencing data. His interest has been combining the laboratory work with bioinformatics for efficient production of scientific information. He founded Genomize at 2015. Currently, He is the CEO of Genomize besides part-time teaching bioinformatics at Bogazici University.


DATE: 07 November 2016, Monday @ 14:40