Virtual Sorting Has a Distinctive Advantage in Identification of Anticorrelated Genes and Further Negative Regulators of Immune Cell Subpopulations

The Journal of Immunology : Official Journal of the American Association of Immunologists
Pingzhang WangDalong Ma

Abstract

Immune cells are highly plastic in both gene expression and cell phenotype. We have established a method of gene expressional plasticity and virtual sorting to evaluate immune cell subpopulations and their characteristic genes in human CD4+ T cells. In this study, we continued to investigate the informatics mechanism on the effectiveness of virtual sorting. We found that virtual sorting had an overall positive correlation to the Pearson correlation in the identification of positively correlated genes. However, owing to nonlinear biological anticorrelation, virtual sorting showed a distinctive advantage for anticorrelated genes, suggesting an important role in the identification of negative regulators. In addition, based on virtual sorting results, we identified two basic gene sets among highly plastic genes, i.e., highly plastic cell cycle-associated molecules and highly plastic immune and defense response-associated molecules. Genes within each set tended to be positively connected, but genes between two sets were often anticorrelated. Further analysis revealed preferential transcription factor binding motifs existed between highly plastic cell cycle-associated molecules and highly plastic immune and defense response-associate...Continue Reading

References

Jun 6, 2002·Proceedings of the National Academy of Sciences of the United States of America·Sanjit K RoyDhananjaya V Kalvakolanu
Nov 13, 2004·The EMBO Journal·Claire AttwoollKristian Helin
Sep 17, 2005·American Journal of Respiratory Cell and Molecular Biology·Babett BartlingAndreas Simm
Jul 16, 2008·The Journal of Experimental Medicine·Götz R A EhrhardtMax D Cooper
Dec 26, 2008·The Journal of Immunology : Official Journal of the American Association of Immunologists·Alexandre CloutierPatrick P McDonald
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Mar 19, 2009·Journal of Translational Medicine·Louis J SparveroMichael T Lotze
Jul 16, 2009·Journal of Cellular Physiology·Gareth Brady, Paul J Farrell
May 21, 2010·The Journal of Immunology : Official Journal of the American Association of Immunologists·Gang ChenJeffrey A Whitsett
Jul 21, 2010·Nature Immunology·Kenneth M Murphy, Brigitta Stockinger
Sep 29, 2011·Immunity·Daigo HashimotoMiriam Merad
Sep 29, 2011·The Journal of Immunology : Official Journal of the American Association of Immunologists·Rahul KushwahJim Hu
May 16, 2012·The Journal of Immunology : Official Journal of the American Association of Immunologists·Wenjie HuangQinxue Hu
Jul 12, 2013·Nature Reviews. Cancer·Subhashini Sadasivam, James A DeCaprio
Aug 12, 2014·Nucleic Acids Research·Gerd A MüllerKurt Engeland
Oct 19, 2014·Nucleic Acids Research·Pingzhang WangDalong Ma
Nov 2, 2014·Nucleic Acids Research·Sipko van DamJoão Pedro de Magalhães
Nov 16, 2014·The Journal of Immunology : Official Journal of the American Association of Immunologists·Shinya TanakaChen Dong
Mar 15, 2015·BMC Genomics·Lauren A SolomonRodney P DeKoter
May 20, 2015·Scientific Reports·Pingzhang WangDalong Ma
Jun 13, 2015·Nature Reviews. Immunology·Nicolas SerafiniJames P Di Santo
Jun 13, 2015·Nature Reviews. Immunology·Ping Shen, Simon Fillatreau
Jul 25, 2015·Nature Reviews. Immunology·E John Wherry, Makoto Kurachi
Sep 1, 2015·Nature Immunology·Hiroko NakatsukasaWanJun Chen
Jun 12, 2016·The Journal of Immunology : Official Journal of the American Association of Immunologists·Pingzhang WangDalong Ma
Aug 5, 2016·BMC Systems Biology·Juli PetereitKaren A Schlauch
Mar 23, 2017·Nature Immunology·Alejandro V VillarinoJohn J O'Shea

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