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Miozzi L, Piro RM, Rosa F, et al. Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PLoS One. 2008;3(6):e2439doi: 10.1371/journal.pone.0002439.
Miozzi, L., Piro, R. M., Rosa, F., Ala, U., Silengo, L., Di Cunto, F., & Provero, P. (2008). Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PloS one, 3(6), e2439. https://doi.org/10.1371/journal.pone.0002439
Miozzi, Laura, et al. "Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data." PloS one vol. 3,6 (2008): e2439. doi: https://doi.org/10.1371/journal.pone.0002439
Miozzi L, Piro RM, Rosa F, Ala U, Silengo L, Di Cunto F, Provero P. Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PLoS One. 2008 Jun 18;3(6):e2439. doi: 10.1371/journal.pone.0002439. PMID: 18560577; PMCID: PMC2409962.
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PLoS One. 2008 Jun 18;3(6):e2439. doi: 10.1371/journal.pone.0002439.

Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

PloS one

Laura Miozzi, Rosario Michael Piro, Fabio Rosa, Ugo Ala, Lorenzo Silengo, Ferdinando Di Cunto, Paolo Provero

Affiliations

  1. Institute of Plant Virology, CNR, Turin, Italy.

PMID: 18560577 PMCID: PMC2409962 DOI: 10.1371/journal.pone.0002439

Abstract

BACKGROUND: High-throughput gene expression data can predict gene function through the "guilt by association" principle: coexpressed genes are likely to be functionally associated.

METHODOLOGY/PRINCIPAL FINDINGS: We analyzed publicly available expression data on normal human tissues. The analysis is based on the integration of data obtained with two experimental platforms (microarrays and SAGE) and of various measures of dissimilarity between expression profiles. The building blocks of the procedure are the Ranked Coexpression Groups (RCG), small sets of tightly coexpressed genes which are analyzed in terms of functional annotation. Functionally characterized RCGs are selected by means of the majority rule and used to predict new functional annotations. Functionally characterized RCGs are enriched in groups of genes associated to similar phenotypes. We exploit this fact to find new candidate disease genes for many OMIM phenotypes of unknown molecular origin.

CONCLUSIONS/SIGNIFICANCE: We predict new functional annotations for many human genes, showing that the integration of different data sets and coexpression measures significantly improves the scope of the results. Combining gene expression data, functional annotation and known phenotype-gene associations we provide candidate genes for several genetic diseases of unknown molecular basis.

References

  1. Genomics. 1992 Jan;12(1):69-73 - PubMed
  2. Am J Med Genet A. 2005 Sep 1;137A(3):292-7 - PubMed
  3. Nat Genet. 2000 May;25(1):25-9 - PubMed
  4. J Biol. 2004;3(5):21 - PubMed
  5. BMC Bioinformatics. 2005 Sep 14;6:227 - PubMed
  6. Eur J Hum Genet. 2002 Aug;10(8):449-56 - PubMed
  7. Neurogenetics. 2006 May;7(2):67-80 - PubMed
  8. Genes Dev. 2003 Feb 15;17(4):419-37 - PubMed
  9. Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7 - PubMed
  10. Genomics. 2005 Oct;86(4):476-88 - PubMed
  11. Hum Mol Genet. 2003 Jul 1;12(13):1631-41 - PubMed
  12. Proc Natl Acad Sci U S A. 2005 May 3;102(18):6368-72 - PubMed
  13. Bioinformatics. 2004 Feb 12;20(3):399-406 - PubMed
  14. Nucleic Acids Res. 2002 Jan 1;30(1):207-10 - PubMed
  15. Nat Rev Genet. 2001 Jun;2(6):418-27 - PubMed
  16. Hum Mutat. 2003 Feb;21(2):170-1 - PubMed
  17. Ann Hum Genet. 2006 May;70(Pt 3):414-6 - PubMed
  18. Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8 - PubMed
  19. Hum Mol Genet. 2006 Mar 1;15(5):767-76 - PubMed
  20. Br J Ophthalmol. 2005 Feb;89(2):198-206 - PubMed
  21. Nucleic Acids Res. 2007 Jan;35(Database issue):D760-5 - PubMed
  22. Nat Genet. 1999 Jan;21(1 Suppl):33-7 - PubMed
  23. Eur J Hum Genet. 2006 May;14(5):535-42 - PubMed

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