OpenLB
Open Library of Bioscience
Advanced Search
Biology
May 16, 2024;13 (5):

DExplore: An Online Tool for Detecting Differentially Expressed Genes from mRNA Microarray Experiments.

Anna D Katsiki, Pantelis E Karatzas, Hector-Xavier De Lastic, Alexandros G Georgakilas, Ourania Tsitsilonis, Constantinos E Vorgias
Author Information
  1. Anna D Katsiki: Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece. ORCID
  2. Pantelis E Karatzas: Unit of Process Control and Informatics, Department of Process Analysis and Plant Design, School of Chemical Engineering, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece.
  3. Hector-Xavier De Lastic: DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece. ORCID
  4. Alexandros G Georgakilas: DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece. ORCID
  5. Ourania Tsitsilonis: Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece. ORCID
  6. Constantinos E Vorgias: Department of Biology, School of Science, National and Kapodistrian University of Athens, 15784 Athens, Greece.
PMID: 38785833 DOI: 10.3390/biology13050351

Abstract

Microarray experiments, a mainstay in gene expression analysis for nearly two decades, pose challenges due to their complexity. To address this, we introduce DExplore, a user-friendly web application enabling researchers to detect differentially expressed genes using data from NCBI's GEO. Developed with R, Shiny, and Bioconductor, DExplore integrates WebGestalt for functional enrichment analysis. It also provides visualization plots for enhanced result interpretation. With a Docker image for local execution, DExplore accommodates unpublished data. To illustrate its utility, we showcase two case studies on cancer cells treated with chemotherapeutic drugs. DExplore streamlines microarray data analysis, empowering molecular biologists to focus on genes of biological significance.

Keywords

bioinformatics differential expression analysis gene enrichment analysis gene expression gene expression profile microarrays response to chemotherapeutics web application

References

  1. Lipids. 2012 Nov;47(11):1019-30 [PMID: 23054549]
  2. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W644-9 [PMID: 15980553]
  3. Nucleic Acids Res. 2019 Jul 2;47(W1):W199-W205 [PMID: 31114916]
  4. Biostatistics. 2003 Apr;4(2):249-64 [PMID: 12925520]
  5. Nucleic Acids Res. 2003 Feb 15;31(4):e15 [PMID: 12582260]
  6. Nucleic Acids Res. 2023 Jul 5;51(W1):W207-W212 [PMID: 37144459]
  7. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W457-9 [PMID: 15215429]
  8. Pharmacogenet Genomics. 2011 Jul;21(7):440-6 [PMID: 21048526]
  9. Gigascience. 2016 Jul 11;5(1):30 [PMID: 27401684]
  10. Trends Genet. 2006 Feb;22(2):101-9 [PMID: 16380191]
  11. Stat Appl Genet Mol Biol. 2004;3:Article3 [PMID: 16646809]
  12. Nat Biotechnol. 2017 Apr;35(4):342-346 [PMID: 28288103]
  13. BMC Bioinformatics. 2008 Jan 24;9:46 [PMID: 18218103]
  14. Bioinformatics. 2018 May 1;34(9):1600-1602 [PMID: 29069305]
  15. BMC Bioinformatics. 2004 Aug 14;5:111 [PMID: 15310390]
  16. Front Plant Sci. 2023 Dec 19;14:1250728 [PMID: 38169825]
  17. Mutat Res. 2015 Mar;773:9-15 [PMID: 25705119]
  18. Pathol Res Pract. 2023 Nov;251:154838 [PMID: 37804544]
  19. Nat Genet. 1999 Jan;21(1 Suppl):10-4 [PMID: 9915494]
  20. Physiol Genomics. 2006 May 16;25(3):355-63 [PMID: 16554544]
  21. Nucleic Acids Res. 2015 Apr 20;43(7):e47 [PMID: 25605792]
  22. Nat Genet. 2000 May;25(1):25-9 [PMID: 10802651]
  23. Cell J. 2023 Dec 31;25(12):874-882 [PMID: 38192258]
  24. Bioinformatics. 2014 Feb 15;30(4):523-30 [PMID: 24336805]
  25. Cell Death Dis. 2021 Apr 1;12(4):339 [PMID: 33795647]
  26. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W741-8 [PMID: 15980575]
  27. PeerJ. 2015 Sep 24;3:e1273 [PMID: 26421241]
  28. Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):18060-5 [PMID: 23077249]
  29. Bioinformatics. 2005 Sep 15;21(18):3587-95 [PMID: 15994189]
  30. Bioinformatics. 2004 Aug 12;20(12):1971-3 [PMID: 15073026]
  31. Bioinformatics. 2010 Oct 1;26(19):2363-7 [PMID: 20688976]
  32. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5 [PMID: 23193258]
  33. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W308-14 [PMID: 18508806]
  34. J Nutr. 2019 Jan 1;149(1):46-56 [PMID: 30601995]
  35. Elife. 2012 Dec 18;1:e00387 [PMID: 23256047]
  36. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W498-503 [PMID: 16845058]
  37. Microb Biotechnol. 2018 Jul;11(4):588-605 [PMID: 29806194]
  38. Stat Appl Genet Mol Biol. 2003;2:Article1 [PMID: 16646779]
  39. Biol Direct. 2015 Sep 03;10:46 [PMID: 26335588]
  40. Bioinformatics. 2007 Jul 15;23(14):1846-7 [PMID: 17496320]
  41. Mol Genet Genomics. 2020 Nov;295(6):1355-1368 [PMID: 32661593]
  42. Nucleic Acids Res. 2009 Jan;37(1):1-13 [PMID: 19033363]
  43. Nucleic Acids Res. 2015 Jul 1;43(W1):W117-21 [PMID: 25897133]
  44. Nat Methods. 2015 Feb;12(2):115-21 [PMID: 25633503]
  45. Nucleic Acids Res. 2019 Jan 8;47(D1):D330-D338 [PMID: 30395331]
  46. Bioinformatics. 2003 Jan 22;19(2):185-93 [PMID: 12538238]
  47. Nat Genet. 2009 Feb;41(2):149-55 [PMID: 19174838]
  48. Pediatr Nephrol. 2009 Sep;24(9):1643-59; quiz 1655, 1659 [PMID: 18568367]
  49. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W465-70 [PMID: 15215431]

Grants

  1. SARG-NKUA project #14210/National and Kapodistrian University of Athens
  2. project 21GRD02 BIOSPHERE/European Union
Journal Article
Article has an altmetric score of 2

Word Cloud

Created with Highcharts 10.0.0analysisgeneexpressionDExploredataMicroarraytwowebapplicationgenesenrichmentexperimentsmainstaynearlydecadesposechallengesduecomplexityaddressintroduceuser-friendlyenablingresearchersdetectdifferentiallyexpressedusingNCBI'sGEODevelopedRShinyBioconductorintegratesWebGestaltfunctionalalsoprovidesvisualizationplotsenhancedresultinterpretationDockerimagelocalexecutionaccommodatesunpublishedillustrateutilityshowcasecasestudiescancercellstreatedchemotherapeuticdrugsstreamlinesmicroarrayempoweringmolecularbiologistsfocusbiologicalsignificanceDExplore:OnlineToolDetectingDifferentiallyExpressedGenesmRNAExperimentsbioinformaticsdifferentialprofilemicroarraysresponsechemotherapeutics

Similar Articles

Cited By

No available data.