Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data

Journal of the Royal Society, Interface
T MilenkovicN Przulj

Abstract

Many real-world phenomena have been described in terms of large networks. Networks have been invaluable models for the understanding of biological systems. Since proteins carry out most biological processes, we focus on analysing protein-protein interaction (PPI) networks. Proteins interact to perform a function. Thus, PPI networks reflect the interconnected nature of biological processes and analysing their structural properties could provide insights into biological function and disease. We have already demonstrated, by using a sensitive graph theoretic method for comparing topologies of node neighbourhoods called 'graphlet degree signatures', that proteins with similar surroundings in PPI networks tend to perform the same functions. Here, we explore whether the involvement of genes in cancer suggests the similarity of their topological 'signatures' as well. By applying a series of clustering methods to proteins' topological signature similarities, we demonstrate that the obtained clusters are significantly enriched with cancer genes. We apply this methodology to identify novel cancer gene candidates, validating 80 per cent of our predictions in the literature. We also validate predictions biologically by identifying cancer-r...Continue Reading

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Citations

Dec 14, 2011·Bioinformatics·Christopher Whelan, Kemal Sönmez
Sep 11, 2012·Bioinformatics·R W SolavaT Milenkovic
Jan 20, 2011·BMC Bioinformatics·Oleksii KuchaievNataša Pržulj
Jan 18, 2013·BMC Systems Biology·Dario Ghersi, Mona Singh
Sep 18, 2013·BMC Systems Biology·Wynand WinterbachDick de Ridder
Sep 3, 2011·PloS One·Tijana MilenkovićNataša Pržulj
Aug 27, 2013·PloS One·Anida SarajlićNataša Pržulj
Mar 7, 2014·PloS One·Yuriy HulovatyyTijana Milenković
Apr 29, 2014·BioMed Research International·Anida Sarajlić, Nataša Pržulj
Sep 18, 2014·BMC Bioinformatics·Kai SunNataša Przulj
Aug 28, 2014·Bioinformatics·Vladimir GligorijevićNataša Pržulj
Feb 21, 2014·Bioinformatics·Fazle E Faisal, Tijana Milenković
Jul 13, 2014·Bioinformatics·Vikram Saraph, Tijana Milenković
Dec 8, 2015·Computers in Biology and Medicine·Hossein RahmaniAndreas Bender
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Fazle Elahi FaisalTijana Milenkovic
Aug 1, 2015·Journal of Ovarian Research·Sheng-Yun CaiMing-Juan Xu
Jun 15, 2015·Bioinformatics·Y HulovatyyT Milenković
Jun 15, 2015·Bioinformatics·Sheng WangJian Peng
Jun 11, 2015·Algorithms for Molecular Biology : AMB·Joseph CrawfordTijana Milenković
Jun 13, 2015·Royal Society Open Science·Omkar SinghPolamarasetty Aparoy
Dec 18, 2013·Bioinformatics·Tomaž Hočevar, Janez Demšar
Aug 8, 2014·Integrative Biology : Quantitative Biosciences From Nano to Macro·Anida SarajlićNataša Pržulj
Apr 27, 2018·PloS One·Robrecht CannoodtYvan Saeys
Jun 14, 2019·Bioinformatics·Sam F L WindelsNataša Pržulj
Dec 29, 2010·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Nataša Pržulj
Jun 4, 2015·EURASIP Journal on Bioinformatics & Systems Biology·Fazle E FaisalTijana Milenković
Jan 13, 2021·Scientific Reports·Antonio Maria FiscarelliPascal Bouvry
Jan 8, 2013·Journal of Chemical Theory and Computation·Djurre H de JongSiewert J Marrink

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