New methods for joint analysis of biological networks and expression data

Bioinformatics
Florian SohlerRalf Zimmer

Abstract

Biological networks, such as protein interaction, regulatory or metabolic networks, derived from public databases, biological experiments or text mining can be useful for the analysis of high-throughput experimental data. We present two algorithms embedded in the ToPNet application that show promising performance in analyzing expression data in the context of such networks. First, the Significant Area Search algorithm detects subnetworks consisting of significantly regulated genes. These subnetworks often provide hints on which biological processes are affected in the measured conditions. Second, Pathway Queries allow detection of networks including molecules that are not necessarily significantly regulated, such as transcription factors or signaling proteins. Moreover, using these queries, the user can formulate biological hypotheses and check their validity with respect to experimental data. All resulting networks and pathways can be explored further using the interactive analysis tools provided by ToPNet program.

Citations

Sep 21, 2013·Nature Reviews. Genetics·Koyel MitraTrey Ideker
Mar 1, 2012·IET Systems Biology·Z-P LiuL Chen
Oct 15, 2008·SAR and QSAR in Environmental Research·A KelE Wingender
Jul 18, 2006·Bioinformatics·Pall F Jonsson, Paul A Bates
Dec 5, 2006·Bioinformatics·Katrin FundelRalf Zimmer
Feb 3, 2007·Bioinformatics·Serban NacuSusan Holmes
Aug 13, 2011·Bioinformatics·Orland Gonzalez, Ralf Zimmer
Sep 1, 2007·Current Opinion in Rheumatology·Thomas AignerRalf Zimmer
Jul 20, 2007·Journal of Bioinformatics and Computational Biology·Andrey Y SivachenkoIlya Mazo
Jan 15, 2011·BMC Bioinformatics·Sohyun HwangDoheon Lee
Feb 13, 2013·BMC Bioinformatics·Raj K GaireIzhak Haviv
Jan 20, 2012·BMC Systems Biology·Liang-Chun ChenVon-Wun Soo
Feb 26, 2014·BMC Systems Biology·Hui YuZhongming Zhao
Mar 28, 2009·PLoS Computational Biology·Sonia M LeachLawrence Hunter
Jan 17, 2012·Proteomics·Wilson W B GohLimsoon Wong
May 26, 2015·Frontiers in Bioengineering and Biotechnology·Giovanni MicaleRosalba Giugno
Nov 28, 2014·Nucleic Acids Research·Guy E ZinmanZiv Bar-Joseph
Jul 9, 2005·Journal of Biochemistry·G V HarshaRaniUpinder S Bhalla
Jun 21, 2006·The Journal of Immunology : Official Journal of the American Association of Immunologists·Jennifer A FulcherBenhur Lee

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