Bilkent University
Department of Computer Engineering


Construction and comparison of gene expression networks through normal and cancer states


Pegah Khosravi, PhD
Institute for Research in Fundamental Sciences, Iran

Cancer is a main health problem in many countries, yet the molecular changes that drive its progression are not fully understood, so the study of cancer is a challenging task in Bioinformatics. The availability of high-throughput gene expression data has led to the development of various computational methods for the identification of key processes involved.

In this project, we show that constructing state-specific gene expression networks provides a powerful alternative strategy for understanding molecular changes that occur during various types of cancers such as prostate cancer. In our approach, we constructed independent networks from each cancerous stage as well as normal and cancer states using a derivative of current state-of-art reverse engineering approaches. We next highlighted crucial pathways and Gene Ontology (GO) involved in different types of cancers. We showed that such perturbations in these networks can be efficiently detected by analyzing each network individually and also in comparison with each other.

Using this novel approach, our results led to the detection of 49 critical pathways and GOs related to prostate cancer, many of which were previously shown to be involved in this cancer. Correct inference of the processes and master regulators that mediate molecular changes during cancer progression is one of the major challenges in cancer genomics. In this work, we used a network-based approach to this problem. Application of our approach to the cancer data has led to the re-establishment of previous knowledge about this complex disease, as well as prediction of many other relevant processes and regulators.

Bio: Pegah Khosravi was awarded Bachelor and Master degree in Plants Breeding. Her training in genetics started during the time she worked on her master project. Her zeal in using mathematical modeling and algorithms for describing different biological systems inspired her to pursue a Ph.D in Bioinformatics at Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran in 2009. During her education, she got financial support from the Iranian Ministry of Science scholarship to be a visiting student at Donnelly Center for Cellular and Bimolecular Research, University of Toronto, Canada, for a year. Five years later, she received her PhD in September 2014 and started her first postdoc in October 2014. She is currently a postdoctoral research fellow in the School of Biological Sciences at Institute for Research in Fundamental Sciences (IPM), Tehran, Iran. She also just accepted for a postdoc position at Weill Cornell Medical.

About her projects, they are based on transcriptome data to discover dynamical changes during cancer progression. She analyzes the structural changes in a network during different stages of various cancers ranging from primary tumor to metastasis. She is also trying to develop new algorithms and approaches for detecting critical genes in complex diseases such as cancer. Outside of work, she enjoys hiking, cooking, playing the Santour (Dulcimer), and Nard (Backgammon).


DATE: 19 December 2016, Monday @ 13:40