metaModules identifies key functional subnetworks in microbiome-related disease

Bioinformatics
Ali MaySanne Abeln

Abstract

The human microbiome plays a key role in health and disease. Thanks to comparative metatranscriptomics, the cellular functions that are deregulated by the microbiome in disease can now be computationally explored. Unlike gene-centric approaches, pathway-based methods provide a systemic view of such functions; however, they typically consider each pathway in isolation and in its entirety. They can therefore overlook the key differences that (i) span multiple pathways, (ii) contain bidirectionally deregulated components, (iii) are confined to a pathway region. To capture these properties, computational methods that reach beyond the scope of predefined pathways are needed. By integrating an existing module discovery algorithm into comparative metatranscriptomic analysis, we developed metaModules, a novel computational framework for automated identification of the key functional differences between health- and disease-associated communities. Using this framework, we recovered significantly deregulated subnetworks that were indeed recognized to be involved in two well-studied, microbiome-mediated oral diseases, such as butanoate production in periodontal disease and metabolism of sugar alcohols in dental caries. More importantly, ou...Continue Reading

References

Feb 1, 1987·Journal of Dental Research·M H De Jong, J S Van der Hoeven
Jan 1, 1984·Archives of Oral Biology·D S Harper, W J Loesche
May 1, 1981·Infection and Immunity·R E Singer, B A Buckner
Sep 16, 1999·Journal of Clinical Periodontology·P S LangendijkJ S van der Hoeven
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jan 5, 2001·Journal of Clinical Periodontology·P S LangendijkJ S Van der Hoeven
Aug 10, 2002·Bioinformatics·Trey IdekerAndrew F Siegel
Oct 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Dragana AjdićJoseph J Ferretti
Feb 16, 2005·Proceedings of the National Academy of Sciences of the United States of America·Kiran Raosaheb Patil, Jens Nielsen
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Nov 22, 2005·Lancet·Bruce L PihlstromNewell W Johnson
Jan 9, 2007·Lancet·Robert H SelwitzNigel B Pitts
Jan 27, 2007·Genome Research·Daniel H HusonStephan C Schuster
Nov 6, 2008·Nucleic Acids Research·Patricia P Chan, Todd M Lowe
Dec 2, 2008·Nature·Peter J TurnbaughJeffrey I Gordon
Mar 2, 2010·Bioinformatics·Daniela BeisserMarcus T Dittrich
Aug 17, 2010·Bioinformatics·Robert C Edgar
Feb 10, 2011·Nature Reviews. Gastroenterology & Hepatology·Si Ming ManHazel M Mitchell
Jul 1, 2011·The ISME Journal·Pedro Belda-FerreAlex Mira
Jan 3, 2012·Current Opinion in Microbiology·Christopher M Rath, Pieter C Dorrestein
Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Adrian MarchettiE Virginia Armbrust
Jun 16, 2012·Nature·UNKNOWN Human Microbiome Project Consortium
Jun 22, 2012·PLoS Computational Biology·Sahar AbubuckerCurtis Huttenhower
Aug 18, 2012·Advances in Dental Research·R A BurneM M Nascimento
Sep 28, 2012·Genome Biology·Xochitl C MorganCurtis Huttenhower
Oct 17, 2012·Bioinformatics·Evguenia KopylovaHélène Touzet
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
Sep 21, 2013·Nature Reviews. Genetics·Koyel MitraTrey Ideker
Sep 26, 2013·Methods in Enzymology·Chengwei LuoKonstantinos T Konstantinidis
May 21, 2014·Proceedings of the National Academy of Sciences of the United States of America·Eric A FranzosaCurtis Huttenhower
Jul 9, 2014·BMC Bioinformatics·Kasper DinklaGunnar W Klau
Sep 2, 2014·Frontiers in Cellular and Infection Microbiology·Scott N PetersonWalter A Bretz
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Jan 7, 2015·Nature·Losee L LingKim Lewis

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Citations

Feb 18, 2016·Briefings in Bioinformatics·Wei MaQinghua Cui
Oct 22, 2016·Scientific Reports·Ranjith RajendranGordon Ramage
Mar 9, 2018·Journal of Dental Research·J Solbiati, J Frias-Lopez
Mar 21, 2018·Genes & Nutrition·Bastian HornungPeter J Schaap
Sep 28, 2017·NPJ Systems Biology and Applications·Kieu Trinh DoJan Krumsiek
Nov 24, 2020·Periodontology 2000·Ana E Duran-Pinedo

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