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Huang Y, Chang Z, Li X, et al. Integrated multifactor analysis explores core dysfunctional modules in autism spectrum disorder. Int J Biol Sci. 2018;14(8):811-818doi: 10.7150/ijbs.24624.
Huang, Y., Chang, Z., Li, X., Liang, S., Yi, Y., & Wu, L. (2018). Integrated multifactor analysis explores core dysfunctional modules in autism spectrum disorder. International journal of biological sciences, 14(8), 811-818. https://doi.org/10.7150/ijbs.24624
Huang, Yan, et al. "Integrated multifactor analysis explores core dysfunctional modules in autism spectrum disorder." International journal of biological sciences vol. 14,8 (2018): 811-818. doi: https://doi.org/10.7150/ijbs.24624
Huang Y, Chang Z, Li X, Liang S, Yi Y, Wu L. Integrated multifactor analysis explores core dysfunctional modules in autism spectrum disorder. Int J Biol Sci. 2018 May 22;14(8):811-818. doi: 10.7150/ijbs.24624. eCollection 2018. PMID: 29989084; PMCID: PMC6036758.
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Int J Biol Sci. 2018 May 22;14(8):811-818. doi: 10.7150/ijbs.24624. eCollection 2018.

Integrated multifactor analysis explores core dysfunctional modules in autism spectrum disorder.

International journal of biological sciences

Yan Huang, Zhenghong Chang, Xiaodan Li, Shuang Liang, Ying Yi, Lijie Wu

Affiliations

  1. Department of Child and Adolescent Health, School of Public Health, Harbin Medical University, Harbin, China.
  2. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.

PMID: 29989084 PMCID: PMC6036758 DOI: 10.7150/ijbs.24624

Abstract

Autism spectrum disorder (ASD) is a complex neurodevelopmental disease in early childhood, and growing up to be a major cause of disability in children. However, the underlying molecular mechanism of ASD remains elusive. Hence, we represented integrated multifactor analysis exploring dysfunctional modules based on RNA-Seq data from corpus callosum in 6 patients with ASD and 6 normal individuals. According to protein-protein interactions (PPIs) and WGCNA, we performed co-expression modules analysis for ASD-associated genes, and identified 25 modules with differentially expressed genes (DEGs), observing that genes in these modules were significantly involved in various biological processes in nervous system, sensory system, phylogenetic system and variety of signaling pathways. Then, based on transcriptional and post-transcriptional regulations, integrating transcription factor (TF)-target and RNA-associated interactions, significant regulators of co-expression modules were identified as pivot regulators, including 67 pivot TFs, 13 pivot miRNAs and 6 pivot lncRNAs. GO and KEGG pathway enrichment analysis demonstrated that the pivot miRNAs significantly enriched in neural or mental-associated biological progresses. The pivot TFs were mainly involved in various regulation of transcription, immune system and organs development. Finally, our work deciphered a multifactor dysfunctional co-expression subnetwork involved in ASD, helps uncover core dysfunctional modules for this disease and improves our understanding of its underlying molecular mechanism.

Keywords: Autism spectrum disorder; Co-expression; Core dysfunctional module; Multifactor analysis

Conflict of interest statement

Competing Interests: The authors have declared that no competing interest exists.

References

  1. Neuro Endocrinol Lett. 2016 Nov;37(6):439-444 - PubMed
  2. J Exp Med. 2016 Jun 27;213(7):1267-84 - PubMed
  3. IEEE/ACM Trans Comput Biol Bioinform. 2016 Apr 05;:null - PubMed
  4. Nucleic Acids Res. 2017 Jan 4;45(D1):D362-D368 - PubMed
  5. Mol Syst Biol. 2014 Dec 30;10:774 - PubMed
  6. J Alzheimers Dis. 2014;40(4):1017-27 - PubMed
  7. Medwave. 2017 Aug 28;17(7):e7031 - PubMed
  8. Nat Rev Genet. 2007 Feb;8(2):93-103 - PubMed
  9. Tumour Biol. 2015 Feb;36(2):503-13 - PubMed
  10. Dev Biol. 2009 Nov 1;335(1):78-92 - PubMed
  11. PLoS Comput Biol. 2017 May 8;13(5):e1005535 - PubMed
  12. Brief Funct Genomics. 2016 Jan;15(1):55-64 - PubMed
  13. Genet Mol Biol. 2014 Mar;37(1 Suppl):210-9 - PubMed
  14. PLoS One. 2013 Jul 29;8(7):e69807 - PubMed
  15. Genes Dev. 2015 Jul 1;29(13):1343-55 - PubMed
  16. Cell. 2013 Nov 21;155(5):1008-21 - PubMed
  17. Mol Neurobiol. 2017 Nov;54(9):6820-6826 - PubMed
  18. Nature. 2014 Nov 13;515(7526):216-21 - PubMed
  19. Nat Biotechnol. 2015 Mar;33(3):290-5 - PubMed
  20. Nucleic Acids Res. 2009 Jan;37(1):1-13 - PubMed
  21. Cancer Res. 2011 Feb 1;71(3):852-61 - PubMed
  22. Mol Biol Evol. 2003 Sep;20(9):1377-419 - PubMed
  23. Genes Dev. 2001 Sep 15;15(18):2343-60 - PubMed
  24. Cell Res. 2012 Sep;22(9):1322-4 - PubMed
  25. Genome Res. 2009 Jan;19(1):92-105 - PubMed
  26. Nat Rev Genet. 2008 May;9(5):341-55 - PubMed
  27. Dialogues Clin Neurosci. 2009;11(1):35-43 - PubMed
  28. Am J Med Genet A. 2015 Jan;167A(1):169-73 - PubMed
  29. Nature. 2003 Jul 10;424(6945):147-51 - PubMed
  30. BMC Bioinformatics. 2008 Dec 29;9:559 - PubMed
  31. Trends Genet. 2016 Mar;32(3):139-146 - PubMed
  32. Bioinformatics. 2018 Feb 1;34(3):398-406 - PubMed
  33. Nucleic Acids Res. 2017 Jan 4;45(D1):D115-D118 - PubMed
  34. Nat Methods. 2015 Apr;12(4):357-60 - PubMed
  35. Annu Rev Clin Psychol. 2015;11:53-70 - PubMed
  36. PLoS One. 2013 Oct 03;8(10):e75682 - PubMed
  37. Nat Commun. 2014 Nov 24;5:5595 - PubMed
  38. Nucleic Acids Res. 2018 Jan 4;46(D1):D380-D386 - PubMed
  39. Mol Syst Biol. 2007;3:104 - PubMed
  40. CNS Neurosci Ther. 2016 Oct;22(10):845-53 - PubMed
  41. Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5 - PubMed
  42. Mol Cytogenet. 2016 Dec 3;9:89 - PubMed
  43. Nature. 2011 May 25;474(7351):380-4 - PubMed
  44. Genes Dev. 2007 Jul 1;21(13):1636-52 - PubMed
  45. Genome Res. 2011 Aug;21(8):1260-72 - PubMed
  46. JAMA Neurol. 2016 Oct 1;73(10):1255 - PubMed
  47. Nucleic Acids Res. 2015 Jan;43(Database issue):D76-81 - PubMed
  48. J Neurosci. 2008 Oct 15;28(42):10576-86 - PubMed
  49. Nat Neurosci. 2016 Nov;19(11):1454-1462 - PubMed
  50. Dev Biol. 2007 Mar 15;303(2):784-99 - PubMed
  51. Nucleic Acids Res. 2015 Jul 1;43(W1):W460-6 - PubMed
  52. Nature. 2016 Dec 15;540(7633):423-427 - PubMed

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