Importance of correlation between gene expression levels: Application to the type i interferon signature in rheumatoid arthritis

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Reynier, Frédéric ^a   Petit, Fabien ^a   Paye, Malick ^a   Turrel Davin, Fanny ^a   Imbert, Pierre Emmanuel ^a   Hot, Arnaud ^a   Mougin, Bruno ^a   Miossec, Pierre ^a,b  

^a EDOUARD HERRIOT HOSPITAL   (France)

^b University of Lyon   (France)

Author keywords

[No Author keywords available]

Indexed keywords

INTERFERON; TUMOR NECROSIS FACTOR INHIBITOR; METHOTREXATE;

ADULT; ARTICLE; BLOOD SAMPLING; CLASSIFICATION ALGORITHM; CLASSIFICATION ALGORITHM BASED ON A BIOLOGICAL SIGNATURE; CONTROLLED STUDY; CORRELATIONAL STUDY; FEMALE; GENE; GENE ACTIVITY; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC CORRELATION; GENETIC HETEROGENEITY; HUMAN; MAJOR CLINICAL STUDY; MALE; RHEUMATOID ARTHRITIS; SYSTEMIC LUPUS ERYTHEMATOSUS; TYPE 1 IFN GENE; ALGORITHM; BLOOD; CASE CONTROL STUDY; CLUSTER ANALYSIS; DRUG ANTAGONISM; GENE EXPRESSION REGULATION; GENETICS; METHODOLOGY; MIDDLE AGED; PROCEDURES; STANDARD;

ADULT; ALGORITHMS; ARTHRITIS, RHEUMATOID; CASE-CONTROL STUDIES; CLUSTER ANALYSIS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; INTERFERON TYPE I; LUPUS ERYTHEMATOSUS, SYSTEMIC; MALE; METHODS; METHOTREXATE; MIDDLE AGED;

EID: 80054783515     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024828     Document Type: Article

References (37)

1. Kerr MK, (2003) Design considerations for efficient and effective microarray studies. Biometrics 59: 822-828.
2. Wheelan SJ, Martinez Murillo F, Boeke JD, (2008) The incredible shrinking world of DNA microarrays. Mol Biosyst 4: 726-732.
3. Eisen MB, Spellman PT, Brown PO, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
4. Ben-Dor A, Chor B, Karp R, Yakhini Z, (2003) Discovering local structure in gene expression data: the order-preserving submatrix problem. J Comput Biol 10: 373-384.
5. Cheng Y, Church GM, (2000) Biclustering of expression data. Proc Int Conf Intell Syst Mol Biol 8: 93-103.
6. Madeira SC, Oliveira AL, (2004) Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans Comput Biol Bioinform 1: 24-45.
7. van der Pouw Kraan TC, van Gaalen FA, Huizinga TW, Pieterman E, Breedveld FC, et al. (2003) Discovery of distinctive gene expression profiles in rheumatoid synovium using cDNA microarray technology: evidence for the existence of multiple pathways of tissue destruction and repair. Genes Immun 4: 187-196.
8. van der Pouw Kraan TC, van Gaalen FA, Kasperkovitz PV, Verbeet NL, Smeets TJ, et al. (2003) Rheumatoid arthritis is a heterogeneous disease: evidence for differences in the activation of the STAT-1 pathway between rheumatoid tissues. Arthritis Rheum 48: 2132-2145.
9. van der Pouw Kraan TC, Wijbrandts CA, van Baarsen LG, Voskuyl AE, Rustenburg F, et al. (2007) Rheumatoid arthritis subtypes identified by genomic profiling of peripheral blood cells: assignment of a type I interferon signature in a subpopulation of patients. Ann Rheum Dis 66: 1008-1014.
10. Prieto C, Risueño A, Fontanillo C, De las Rivas J, (2008) Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS One 3: e3911.
11. Baechler EC, Batliwalla FM, Karypis G, Gaffney PM, Ortmann WA, et al. (2003) Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc Natl Acad Sci U S A 100: 2610-2615.
12. Tan FK, Zhou X, Mayes MD, Gourh P, Guo X, et al. (2006) Signatures of differentially regulated interferon gene expression and vasculotrophism in the peripheral blood cells of systemic sclerosis patients. Rheumatology (Oxford) 45: 694-702.
13. van Baarsen LG, van der Pouw Kraan TC, Kragt JJ, Baggen JM, Rustenburg F, et al. (2006) A subtype of multiple sclerosis defined by an activated immune defense program. Genes Immun 7: 522-531.
14. Bave U, Nordmark G, Lövgren T, Rönnelid J, Cajander S, et al. (2005) Activation of the type I interferon system in primary Sjögren's syndrome: a possible etiopathogenic mechanism. Arthritis Rheum 52: 1185-1195.
15. Reynier F, Pachot A, Paye M, Xu Q, Turrel-Davin F, et al. (2010) Specific gene expression signature associated with development of autoimmune type-I diabetes using whole-blood microarray analysis. Genes Immun 11: 269-278.
16. Huang X, Yuang J, Goddard A, Foulis A, James RF, et al. (1995) Interferon expression in the pancreases of patients with type I diabetes. Diabetes 44: 658-664.
17. Greenberg SA, Pinkus JL, Pinkus GS, Burleson T, Sanoudou D, et al. (2005) Interferon-alpha/beta-mediated innate immune mechanisms in dermatomyositis. Ann Neurol 57: 664-678.
18. Baechler EC, Bauer JW, Slattery CA, Ortmann WA, Espe KJ, et al. (2007) An interferon signature in the peripheral blood of dermatomyositis patients is associated with disease activity. Mol Med 13: 59-68.
19. Kirou KA, Lee C, George S, Louca K, Papagiannis IG, et al. (2004) Coordinate overexpression of interferon-alpha-induced genes in systemic lupus erythematosus. Arthritis Rheum 50: 3958-3967.
20. Bauer JW, Baechler EC, Petri M, Batliwalla FM, Crawford D, et al. (2006) Elevated serum levels of interferon-regulated chemokines are biomarkers for active human systemic lupus erythematosus. PLoS Med 3: e491.
21. Chou JW, Zhou T, Kaufmann WK, Paules RS, Bushel PR, (2007) Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes. BMC Bioinformatics 8: 427.
22. Ning S, Huye LE, Pagano JS, (2005) Regulation of the transcriptional activity of the IRF7 promoter by a pathway independent of interferon signaling. J Biol Chem 280: 12262-12270.
23. Gugliesi F, Mondini M, Ravera R, Robotti A, de Andrea M, et al. (2005) Up-regulation of the interferon-inducible IFI16 gene by oxidative stress triggers p53 transcriptional activity in endothelial cells. J Leukoc Biol 77: 820-829.
24. Mälarstig A, Sigurdsson S, Eriksson P, Paulsson-Berne G, Hedin U, et al. (2008) Variants of the interferon regulatory factor 5 gene regulate expression of IRF5 mRNA in atherosclerotic tissue but are not associated with myocardial infarction. Arterioscler Thromb Vasc Biol 28: 975-982.
25. Akahoshi M, Nakashima H, Sadanaga A, Miyake K, Obara K, et al. (2008) Promoter polymorphisms in the IRF3 gene confer protection against systemic lupus erythematosus. Lupus 17: 568-574.
26. Palucka AK, Blanck JP, Bennett L, Pascual V, Banchereau J, (2005) Cross-regulation of TNF and IFN-alpha in autoimmune diseases. Proc Natl Acad Sci U S A 102: 3372-3377.
27. Pisetsky DS, (2000) Tumor necrosis factor alpha blockers and the induction of anti-DNA autoantibodies. Arthritis Rheum 43: 2381-2382.
28. Shakoor N, Michalska M, Harris CA, Block JA, (2002) Drug-induced systemic lupus erythematosus associated with etanercept therapy. Lancet 359: 579-580.
29. van Baarsen LG, Wijbrandts CA, Rustenburg F, Cantaert T, van der Pouw Kraan TC, et al. (2010) Regulation of IFN response gene activity during infliximab treatment in rheumatoid arthritis is associated with clinical response to treatment. Arthritis Res Ther 12: R11.
30. Arnett FC, Edworthy SM, Bloch DA, McShane DJ, Fries JF, et al. (1988) The American Rheumatism Association 1987 revised criteria for the classification of rheumatoid arthritis. Arthritis Rheum 31: 315-324.
31. Tan E, Cohen A, Fries J, Masi A, McShane D, et al. (1982) The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 25: 1271-1277.
32. Rainen L, Oelmueller U, Jurgensen S, Wyrich R, Ballas C, et al. (2002) Stabilization of mRNA expression in whole blood samples. Clin Chem 48: 1883-1890.
33. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
34. Bolstad BM, Irizarry RA, Astrand M, Speed TP, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
35. Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, et al. (2005) EXPANDER: an integrative program suite for microarray data analysis. BMC Bioinformatics 21: 6: 232.
36. Tanay A, Sharan R, Shamir R, (2002) Discovering statistically significant biclusters in gene expression data. Bioinformatics 18 (Suppl 1): S136-144.
37. Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV, et al. (2005) A network-based analysis of systemic inflammation in humans. Nature 437: 1032-1037.