The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways

BMC Bioinformatics
Yahui SunSaman Halgamuge

Abstract

Cancer constitutes a momentous health burden in our society. Critical information on cancer may be hidden in its signaling pathways. However, even though a large amount of money has been spent on cancer research, some critical information on cancer-related signaling pathways still remains elusive. Hence, new works towards a complete understanding of cancer-related signaling pathways will greatly benefit the prevention, diagnosis, and treatment of cancer. We propose the node-weighted Steiner tree approach to identify important elements of cancer-related signaling pathways at the level of proteins. This new approach has advantages over previous approaches since it is fast in processing large protein-protein interaction networks. We apply this new approach to identify important elements of two well-known cancer-related signaling pathways: PI3K/Akt and MAPK. First, we generate a node-weighted protein-protein interaction network using protein and signaling pathway data. Second, we modify and use two preprocessing techniques and a state-of-the-art Steiner tree algorithm to identify a subnetwork in the generated network. Third, we propose two new metrics to select important elements from this subnetwork. On a commonly used personal co...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Nov 3, 2001·Physical Review Letters·V Latora, M Marchiori
Jan 10, 2003·Nucleic Acids Research·Gary D BaderChristopher W V Hogue
Apr 30, 2003·Cell Death and Differentiation·M Oren
Oct 31, 2003·Cancer Cell·Ji LuoLewis C Cantley
Mar 17, 2004·Cancer Treatment Reviews·Juan Angel Fresno VaraManuel González-Barón
Oct 27, 2004·Apoptosis : an International Journal on Programmed Cell Death·M OsakiH Ito
Jan 20, 2005·Bioinformatics·Kevin R Brown, Igor Jurisica
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Jun 27, 2006·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·Kurt BommertThorsten Stühmer
Jun 28, 2006·The Journal of Experimental Medicine·Hidetoshi SumimotoYutaka Kawakami
Jul 3, 2007·Cell·Brendan D Manning, Lewis C Cantley
Apr 16, 2008·Nucleic Acids Research·Xing-Ming ZhaoKazuyuki Aihara
Mar 19, 2009·Molecular Systems Biology·Nir YosefRoded Sharan
May 11, 2010·Molecular Aspects of Medicine·Alexander Levitzki, Shoshana Klein
Nov 13, 2010·Nucleic Acids Research·Ethan G CeramiChris Sander
Dec 1, 2010·Bioinformatics·Guy Geva, Roded Sharan
Mar 23, 2011·Nature Neuroscience·Ying ChenQ Richard Lu
Mar 21, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Shuichi KawanoSatoru Miyano
Aug 18, 2012·Current Opinion in Cell Biology·Maria Felice BrizziPaola Defilippi
Dec 25, 2012·Nature Cell Biology·Patricia A J Muller, Karen H Vousden
Feb 2, 2013·Science·Gregor NeuertAlexander van Oudenaarden
Feb 7, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Nurcan TuncbagErnest Fraenkel
Mar 8, 2013·Nature Reviews. Cancer·Kieran F HarveyDavid M Thomas
May 1, 2013·BMC Bioinformatics·Afshin Sadeghi, Holger Fröhlich
Sep 11, 2013·PLoS Biology·Sulakshana P MukherjeeGourisankar Ghosh
Apr 11, 2014·JAMA Psychiatry·John I NurnbergerUNKNOWN Psychiatric Genomics Consortium Bipolar Group
Oct 30, 2014·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Jan 30, 2015·Database : the Journal of Biological Databases and Curation·Saikat Chowdhury, Ram Rup Sarkar
Apr 27, 2016·Journal of Theoretical Biology·Yang LiuZhen Wang
Oct 11, 2017·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Anna RitzT M Murali

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Citations

Dec 4, 2019·BMC Bioinformatics·Ibrahim YoussefAnna Ritz

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Methods Mentioned

BETA
Co-immunoprecipitation

Software Mentioned

String
DIMACS
Pathway Commons
OPHID
Reactome
PANTHER

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