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Karami H, Derakhshani A, Ghasemigol M, et al. Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection. J Clin Med. 2021;10(16)doi: 10.3390/jcm10163567.
Karami, H., Derakhshani, A., Ghasemigol, M., Fereidouni, M., Miri-Moghaddam, E., Baradaran, B., Tabrizi, N. J., Najafi, S., Solimando, A. G., Marsh, L. M., Silvestris, N., De Summa, S., Paradiso, A. V., Racanelli, V., & Safarpour, H. (2021). Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection. Journal of clinical medicine, 10(16), . https://doi.org/10.3390/jcm10163567
Karami, Hassan, et al. "Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection." Journal of clinical medicine vol. 10,16 (2021). doi: https://doi.org/10.3390/jcm10163567
Karami H, Derakhshani A, Ghasemigol M, Fereidouni M, Miri-Moghaddam E, Baradaran B, Tabrizi NJ, Najafi S, Solimando AG, Marsh LM, Silvestris N, De Summa S, Paradiso AV, Racanelli V, Safarpour H. Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection. J Clin Med. 2021 Aug 13;10(16). doi: 10.3390/jcm10163567. PMID: 34441862; PMCID: PMC8397209.
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J Clin Med. 2021 Aug 13;10(16). doi: 10.3390/jcm10163567.

Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection.

Journal of clinical medicine

Hassan Karami, Afshin Derakhshani, Mohammad Ghasemigol, Mohammad Fereidouni, Ebrahim Miri-Moghaddam, Behzad Baradaran, Neda Jalili Tabrizi, Souzan Najafi, Antonio Giovanni Solimando, Leigh M Marsh, Nicola Silvestris, Simona De Summa, Angelo Virgilio Paradiso, Vito Racanelli, Hossein Safarpour

Affiliations

  1. Student Research Committee, Birjand University of Medical Sciences, Birjand 9717853577, Iran.
  2. Laboratory of Experimental Pharmacology, IRCCS-Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy.
  3. Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran.
  4. Department of Computer Engineering, University of Birjand, Birjand 9717434765, Iran.
  5. Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand 9717853577, Iran.
  6. Cardiovascular Diseases Research Center & Department of Molecular Medicine, School of Medicine, Birjand University of Medical Sciences, Birjand 9717853577, Iran.
  7. Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran.
  8. Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", 70121 Bari, Italy.
  9. Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstraße 6/VI, 8010 Graz, Austria.
  10. Medical Oncology Unit, IRCCS-Istituto Tumori "Giovanni Paolo II" of Bari, 70124 Bari, Italy.
  11. Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori 'Giovanni Paolo II', 70124 Bari, Italy.
  12. National Cancer Research Centre, Istituto Tumori G Paolo II, 70124 Bari, Italy.

PMID: 34441862 PMCID: PMC8397209 DOI: 10.3390/jcm10163567

Abstract

The coronavirus disease-2019 (COVID-19) pandemic has caused an enormous loss of lives. Various clinical trials of vaccines and drugs are being conducted worldwide; nevertheless, as of today, no effective drug exists for COVID-19. The identification of key genes and pathways in this disease may lead to finding potential drug targets and biomarkers. Here, we applied weighted gene co-expression network analysis and LIME as an explainable artificial intelligence algorithm to comprehensively characterize transcriptional changes in bronchial epithelium cells (primary human lung epithelium (NHBE) and transformed lung alveolar (A549) cells) during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Our study detected a network that significantly correlated to the pathogenicity of COVID-19 infection based on identified hub genes in each cell line separately. The novel hub gene signature that was detected in our study, including

Keywords: COVID-19; SARS-CoV-2; WGCNA; bronchial epithelium cells; explainable artificial intelligence; transcriptional profiling; treatment

References

  1. Gene. 2019 Aug 20;710:122-130 - PubMed
  2. Front Genet. 2020 Jun 09;11:641 - PubMed
  3. Comput Struct Biotechnol J. 2014 Sep 03;11(18):22-7 - PubMed
  4. Nat Med. 2020 Apr;26(4):450-452 - PubMed
  5. Virus Res. 2021 Sep;302:198469 - PubMed
  6. Viruses. 2020 Jul 20;12(7): - PubMed
  7. Turk J Biol. 2020 Jun 21;44(3):168-177 - PubMed
  8. Crit Rev Microbiol. 2020 Nov;46(6):689-702 - PubMed
  9. Cancers (Basel). 2021 May 17;13(10): - PubMed
  10. Epigenomics. 2020 Nov;12(22):1969-1981 - PubMed
  11. Lancet. 2020 Feb 15;395(10223):514-523 - PubMed
  12. Front Cell Dev Biol. 2020 Jul 17;8:677 - PubMed
  13. Nature. 2020 Mar;579(7798):270-273 - PubMed
  14. Annu Rev Med. 2017 Jan 14;68:387-399 - PubMed
  15. Nat Rev Immunol. 2020 Jun;20(6):345-346 - PubMed
  16. Bone. 2011 Jul;49(1):42-9 - PubMed
  17. Antimicrob Agents Chemother. 2020 Jun 23;64(7): - PubMed
  18. N Engl J Med. 2020 May 7;382(19):1787-1799 - PubMed
  19. Front Immunol. 2019 Sep 20;10:2106 - PubMed
  20. Viruses. 2020 Apr 06;12(4): - PubMed
  21. Lancet Respir Med. 2020 Apr;8(4):420-422 - PubMed
  22. Intensive Care Med. 2020 Feb;46(2):315-328 - PubMed
  23. Cell Host Microbe. 2016 Feb 10;19(2):181-93 - PubMed
  24. Drug Discov Ther. 2020;14(1):58-60 - PubMed
  25. J Cell Biochem. 2018 Sep;119(9):7687-7695 - PubMed
  26. Exp Eye Res. 2010 Jan;90(1):130-6 - PubMed
  27. J Infect Dis. 2020 Jul 23;222(4):556-563 - PubMed
  28. Curr Top Microbiol Immunol. 2013;372:173-91 - PubMed
  29. Semin Immunopathol. 2016 Jul;38(4):471-82 - PubMed
  30. J Immunol. 2002 Apr 1;168(7):3577-85 - PubMed
  31. Emerg Microbes Infect. 2020 Dec;9(1):761-770 - PubMed
  32. Sci Rep. 2021 Feb 24;11(1):4495 - PubMed
  33. Infect Immun. 2004 Aug;72(8):4410-5 - PubMed
  34. BMC Bioinformatics. 2010 Apr 06;11:170 - PubMed
  35. J Cell Mol Med. 2020 Oct;24(20):12225-12230 - PubMed
  36. J Med Virol. 2006 Apr;78(4):417-24 - PubMed
  37. Exp Ther Med. 2019 Nov;18(5):4067-4075 - PubMed
  38. Life Sci. 2020 Jun 1;250:117583 - PubMed
  39. Clin Dev Immunol. 2013;2013:325412 - PubMed
  40. Sci Rep. 2021 Aug 10;11(1):16212 - PubMed
  41. Sci Rep. 2021 Mar 29;11(1):7052 - PubMed
  42. Front Physiol. 2020 Sep 18;11:555039 - PubMed
  43. Infect Immun. 2019 Jan 24;87(2): - PubMed
  44. Front Mol Biosci. 2019 Nov 22;6:116 - PubMed
  45. Entropy (Basel). 2020 Dec 25;23(1): - PubMed
  46. BMC Infect Dis. 2020 Dec 21;20(1):963 - PubMed
  47. Oncogenesis. 2015 Nov 30;4:e175 - PubMed
  48. Fertil Steril. 2005 May;83(5):1530-5 - PubMed
  49. BMC Biol. 2019 Jul 18;17(1):59 - PubMed
  50. Infect Drug Resist. 2020 Nov 04;13:3977-3990 - PubMed
  51. Cell. 2020 Aug 6;182(3):685-712.e19 - PubMed
  52. Cell. 2021 Jan 7;184(1):92-105.e16 - PubMed
  53. Genome Res. 2003 Nov;13(11):2498-504 - PubMed
  54. Int J Mol Med. 2020 Oct;46(4):1266-1273 - PubMed
  55. PLoS One. 2019 May 17;14(5):e0217005 - PubMed
  56. Metabolism. 2020 Jul;108:154260 - PubMed
  57. Database (Oxford). 2015 Feb 27;2015: - PubMed
  58. Genome Biol. 2004;5(10):R80 - PubMed
  59. Nat Commun. 2020 Dec 9;11(1):6319 - PubMed
  60. Comput Biol Med. 2020 Nov;126:104051 - PubMed
  61. Signal Transduct Target Ther. 2020 May 29;5(1):84 - PubMed
  62. Nat Rev Microbiol. 2008 Jul;6(7):541-52 - PubMed
  63. Clin Rheumatol. 2020 Jul;39(7):2085-2094 - PubMed
  64. Arch Virol. 2021 Mar;166(3):675-696 - PubMed
  65. JAMA. 2020 Apr 21;323(15):1488-1494 - PubMed
  66. Front Physiol. 2021 Jan 22;11:605792 - PubMed
  67. Int J Mol Sci. 2020 Sep 15;21(18): - PubMed
  68. Science. 2016 Apr 22;352(6284):463-6 - PubMed
  69. Lancet. 2020 Feb 15;395(10223):497-506 - PubMed
  70. Autoimmun Rev. 2020 Jul;19(7):102571 - PubMed
  71. World Allergy Organ J. 2020 Sep;13(9):100454 - PubMed
  72. Cell Physiol Biochem. 2018;48(3):1151-1163 - PubMed
  73. BMC Bioinformatics. 2008 Dec 29;9:559 - PubMed
  74. J Neurol Sci. 2020 Aug 15;415:116935 - PubMed
  75. Eur J Neurol. 2020 Oct 8;: - PubMed
  76. Microbes Infect. 2005 Feb;7(2):248-59 - PubMed
  77. J Transl Med. 2020 Jun 29;18(1):261 - PubMed
  78. PLoS Genet. 2019 May 24;15(5):e1008143 - PubMed
  79. Cell. 2020 May 28;181(5):1036-1045.e9 - PubMed
  80. Iran J Allergy Asthma Immunol. 2020 Oct 18;19(5):517-528 - PubMed
  81. Brief Bioinform. 2021 Mar 22;22(2):1324-1337 - PubMed
  82. Cell Res. 2013 May;23(5):673-90 - PubMed
  83. Nat Immunol. 2015 Dec;16(12):1215-27 - PubMed
  84. Medicine (Baltimore). 2021 Feb 19;100(7):e24321 - PubMed
  85. J Immunol. 2018 Jul 15;201(2):573-582 - PubMed
  86. iScience. 2020 Nov 20;23(11):101697 - PubMed
  87. Cell Host Microbe. 2009 Sep 17;6(3):207-17 - PubMed
  88. Mol Neurodegener. 2015 Oct 05;10:52 - PubMed
  89. J Med Virol. 2012 Jun;84(6):940-6 - PubMed

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