Abstract
Understanding individual patient host-response to viruses is key to designing optimal personalized therapy. Unsurprisingly, in vivo human experimentation to understand individualized dynamic response of the transcriptome to viruses are rarely studied because of the obvious limitations stemming from ethical considerations of the clinical risk. In this rhinovirus study, we first hypothesized that ex vivo human cells response to virus can serve as a proxy for otherwise controversial in vivo human experimentation. We further hypothesized that the N-of-1-pathways framework, previously validated in cancer, can be effective in understanding the more subtle individual transcriptomic response to viral infection. N-of-1-pathways computes a significance score for a given list of gene sets at the patient level, using merely the 'omics profiles of two paired samples as input. We extracted the peripheral blood mononuclear cells (PBMC) of four human subjects, aliquoted in two paired samples, one subjected to ex vivo rhinovirus infection. Their dysregulated genes and pathways were then compared to those of 9 human subjects prior and after intranasal inoculation in vivo with rhinovirus. Additionally, we developed the Similarity Venn Diagram, a ...Continue Reading
References
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
May 10, 2000·Nature Genetics·M AshburnerG Sherlock
Aug 20, 2003·Biostatistics·Rafael A IrizarryTerence P Speed
Jul 1, 2005·Cell Research·Andrea K PerryGenhong Cheng
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Jul 25, 2007·Bioinformatics·Ying TaoYves A Lussier
Nov 27, 2008·Nucleic Acids Research·Da Wei HuangRichard A Lempicki
Aug 12, 2009·Cell Host & Microbe·Aimee K ZaasGeoffrey S Ginsburg
Nov 19, 2009·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
May 7, 2010·Journal of Virology·Pablo R MurciaJames L N Wood
Jan 27, 2011·PloS One·Kathleen H RubinsPatrick O Brown
Mar 23, 2011·Bioinformatics·Xinan YangYves A Lussier
Jan 27, 2012·Journal of the American Medical Informatics Association : JAMIA·Haiquan LiYves A Lussier
Feb 1, 2012·PLoS Computational Biology·Xinan YangYves A Lussier
Jun 14, 2012·PLoS Pathogens·Pablo R MurciaJames L N Wood
Jul 17, 2013·BMC Medical Genomics·James L ChenYves A Lussier
Nov 12, 2013·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Nov 23, 2013·PLoS Medicine·Asuncion MejiasOctavio Ramilo
Jun 9, 2014·Respiratory Research·Jun Young HongMarc B Hershenson
Aug 1, 2014·BMC Medical Genomics·Vincent GardeuxYves A Lussier
Oct 11, 2014·Journal of the American Medical Informatics Association : JAMIA·Vincent GardeuxYves A Lussier
Citations
Feb 3, 2016·Chest·Jodie L SimpsonJohn W Upham
May 14, 2016·Cell Host & Microbe·Angela L Rasmussen, Michael G Katze
Jun 17, 2016·Bioinformatics·A Grant SchisslerYves A Lussier
May 30, 2017·Statistical Methods in Medical Research·A Grant SchisslerYves A Lussier
Feb 29, 2016·BMC Medical Genomics·Niamh M TroyAnthony Bosco
Oct 19, 2017·PloS One·Amanda Barlow-AnackerChristine M Seroogy
Mar 1, 2018·BMC Medical Genomics·Jose L GomezClemente J Britto
Dec 19, 2018·American Journal of Respiratory and Critical Care Medicine·Anya C JonesPatrick G Holt
Jul 13, 2019·BMC Medical Genomics·Samir Rachid ZaimYves A Lussier
Jun 8, 2017·BMC Medical Genomics·Qike LiYves A Lussier
Oct 11, 2017·Journal of the American Medical Informatics Association : JAMIA·Vincent GardeuxYves A Lussier
Jan 6, 2021·Journal of Personalized Medicine·Samir Rachid ZaimYves A Lussier
Feb 26, 2021·PloS One·León Gabriel Gómez-ArchilaElkin Galeano
Dec 23, 2016·Journal of Biomedical Informatics·Qike LiYves A Lussier
Jul 13, 2021·Bioinformatics·Dillon AberasturiYves A Lussier