Gene expression profile based classification models of psoriasis

Genomics

Volumn 103, Issue 1, 2014, Pages 48-55

  Guo, Pi ^a,b,c   Luo, Youxi ^a,b   Mai, Guoqin ^a,b   Zhang, Ming ^f   Wang, Guoqing ^d,e   Zhao, Miaomiao ^a,b   Gao, Liming ^a,b   Li, Fan ^d,e   Zhou, Fengfeng ^a,b  

^a SHENZHEN INSTITUTES OF ADVANCED TECHNOLOGY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c SHANTOU UNIVERSITY MEDICAL COLLEGE   (China)

^d Basic Medical College   (China)

^e JILIN UNIVERSITY   (China)

^f UNIVERSITY OF GEORGIA   (United States)

Author keywords

Classification; Gene expression profiles; Psoriasis

Indexed keywords

ALGORITHM; ARTICLE; C10ORF99 GENE; CLASSIFICATION; CLASSIFIER; CONTROLLED STUDY; GENE EXPRESSION; HUMAN; IGFL1 GENE; MAJOR CLINICAL STUDY; MARKER GENE; MEASUREMENT ACCURACY; PREDICTION; PRIORITY JOURNAL; PSORIASIS; SIGNAL TRANSDUCTION; SUPPORT VECTOR MACHINE;

CLASSIFICATION; GENE EXPRESSION PROFILES; PSORIASIS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CASE-CONTROL STUDIES; CELL PROLIFERATION; DATABASES, FACTUAL; GENE EXPRESSION PROFILING; GENETIC MARKERS; HUMANS; MICROARRAY ANALYSIS; MODELS, GENETIC; PSORIASIS; ROC CURVE; SIGNAL TRANSDUCTION; SKIN; TRANSCRIPTOME;

EID: 84895885338     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2013.11.001     Document Type: Article

References (63)

1. Villasenor-Park J., Wheeler D., Grandinetti L. Psoriasis: evolving treatment for a complex disease. Cleve. Clin. J. Med. 2012, 79:413-423.
2. Chu T.W., Tsai T.F. Psoriasis and cardiovascular comorbidities with emphasis in Asia. G. Ital. Dermatol. Venereol. 2012, 147:189-202.
3. Puig L. Cardiovascular risk and psoriasis: the role of biologic therapy. Actas Dermosifiliogr. 2012, 103:853-862.
4. Gelfand J.M., Dommasch E.D., Shin D.B., Azfar R.S., Kurd S.K., Wang X., Troxel A.B. The risk of stroke in patients with psoriasis. J. Invest. Dermatol. 2009, 129:2411-2418.
5. Vom Berg J., Prokop S., Miller K.R., Obst J., Kalin R.E., Lopategui-Cabezas I., Wegner A., Mair F., Schipke C.G., Peters O., Winter Y., Becher B., Heppner F.L. Inhibition of IL-12/IL-23 signaling reduces Alzheimer's disease-like pathology and cognitive decline. Nat. Med. 2012, 18:1812-1819.
6. Langley R.G., Krueger G.G., Griffiths C.E. Psoriasis: epidemiology, clinical features, and quality of life. Ann. Rheum. Dis. 2005, 64(Suppl. 2):ii18-ii23. (discussion ii24-15).
7. Psoriasis-Aid.com Psoriasis Statistics 2012.
8. Gladman D.D. Natural history of psoriatic arthritis. Baillieres Clin. Rheumatol. 1994, 8:379-394.
9. Chamian F., Lowes M.A., Lin S.L., Lee E., Kikuchi T., Gilleaudeau P., Sullivan-Whalen M., Cardinale I., Khatcherian A., Novitskaya I., Wittkowski K.M., Krueger J.G. Alefacept reduces infiltrating T cells, activated dendritic cells, and inflammatory genes in psoriasis vulgaris. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:2075-2080.
10. Chamian F., Krueger J.G. Psoriasis vulgaris: an interplay of T lymphocytes, dendritic cells, and inflammatory cytokines in pathogenesis. Curr. Opin. Rheumatol. 2004, 16:331-337.
11. Kulski J.K., Kenworthy W., Bellgard M., Taplin R., Okamoto K., Oka A., Mabuchi T., Ozawa A., Tamiya G., Inoko H. Gene expression profiling of Japanese psoriatic skin reveals an increased activity in molecular stress and immune response signals. J. Mol. Med. 2005, 83:964-975.
12. Wikipedia Psoriasis 2012.
13. Gudjonsson J.E., Ding J., Li X., Nair R.P., Tejasvi T., Qin Z.S., Ghosh D., Aphale A., Gumucio D.L., Voorhees J.J., Abecasis G.R., Elder J.T. Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. J. Invest. Dermatol. 2009, 129:2795-2804.
14. Reischl J., Schwenke S., Beekman J.M., Mrowietz U., Sturzebecher S., Heubach J.F. Increased expression of Wnt5a in psoriatic plaques. J. Invest. Dermatol. 2007, 127:163-169.
15. Yao Y., Richman L., Morehouse C., de los Reyes M., Higgs B.W., Boutrin A., White B., Coyle A., Krueger J., Kiener P.A., Jallal B. Type I interferon: potential therapeutic target for psoriasis?. PLoS One 2008, 3:e2737.
16. Swindell W.R., Johnston A., Carbajal S., Han G., Wohn C., Lu J., Xing X., Nair R.P., Voorhees J.J., Elder J.T., Wang X.J., Sano S., Prens E.P., DiGiovanni J., Pittelkow M.R., Ward N.L., Gudjonsson J.E. Genome-wide expression profiling of five mouse models identifies similarities and differences with human psoriasis. PLoS One 2011, 6:e18266.
17. Nair R.P., Duffin K.C., Helms C., Ding J., Stuart P.E., Goldgar D., Gudjonsson J.E., Li Y., Tejasvi T., Feng B.J., Ruether A., Schreiber S., Weichenthal M., Gladman D., Rahman P., Schrodi S.J., Prahalad S., Guthery S.L., Fischer J., Liao W., Kwok P.Y., Menter A., Lathrop G.M., Wise C.A., Begovich A.B., Voorhees J.J., Elder J.T., Krueger G.G., Bowcock A.M., Abecasis G.R., P.Collaborative Association Study of Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Nat. Genet. 2009, 41:199-204.
18. Barrett T., Troup D.B., Wilhite S.E., Ledoux P., Evangelista C., Kim I.F., Tomashevsky M., Marshall K.A., Phillippy K.H., Sherman P.M., Muertter R.N., Holko M., Ayanbule O., Yefanov A., Soboleva A. NCBI GEO: archive for functional genomics data sets-10years on. Nucleic Acids Res. 2011, 39:D1005-D1010.
19. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
20. Benito M., Parker J., Du Q., Wu J., Xiang D., Perou C.M., Marron J.S. Adjustment of systematic microarray data biases. Bioinformatics 2004, 20:105-114.
21. Lauss M., Frigyesi A., Ryden T., Hoglund M. Robust assignment of cancer subtypes from expression data using a uni-variate gene expression average as classifier. BMC Cancer 2010, 10:532.
22. Guyon I., Weston J., Barnhill S., Vapnik V. Gene selection for cancer classification using support vector machines. Mach. Learn. 2002, 46:389-422.
23. Kursa M.B., Rudnicki W.R. Feature selection with the Boruta package. Journal 2010.
24. Liaw A., Wiener M. Classification and regression by randomForest. R News 2002, 2:18-22.
25. Ding Y., Wilkins D. Improving the performance of SVM-RFE to select genes in microarray data. BMC Bioinforma. 2006, 7(Suppl. 2):S12.
26. Furlanello C., Serafini M., Merler S., Jurman G. Entropy-based gene ranking without selection bias for the predictive classification of microarray data. BMC Bioinforma. 2003, 4:54.
27. Furlanello C., Serafini M., Merler S., Jurman G. An accelerated procedure for recursive feature ranking on microarray data. Neural Netw. 2003, 16:641-648.
28. Vapnik V.N. The Nature of Statistical Learning Theory 1999, Springer-Verlag, New York. 2 ed.
29. Swets J.A. Signal Detection Theory and ROC Analysis in Psychology and Diagnostics: Collected Papers 1996, Lawrence Erlbaum Associates, Inc., Hillsdale, NJ, England.
30. Pepe M.S., Longton G., Anderson G.L., Schummer M. Selecting differentially expressed genes from microarray experiments. Biometrics 2003, 59:133-142.
31. Kursa M.B., Rudnicki W.R. Feature selection with the Boruta package. J. Stat. Softw. 2010, 36:1-13.
32. Elizondo D.A., Birkenhead R., Gongora M., Taillard E., Luyima P. Analysis and test of efficient methods for building recursive deterministic perceptron neural networks. Neural Netw. 2007, 20:1095-1108.
33. Li K., Yang M., Sablok G., Fan J., Zhou F. Screening features to improve the class prediction of acute myeloid leukemia and myelodysplastic syndrome. Gene 2013, 512:348-354.
34. Zhou F., Xu Y. cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data. Bioinformatics 2010, 26:2051-2052.
35. Zhou X., Mao J., Ai J., Deng Y., Roth M.R., Pound C., Henegar J., Welti R., Bigler S.A. Identification of plasma lipid biomarkers for prostate cancer by lipidomics and bioinformatics. PLoS One 2012, 7:e48889.
36. Thrift A.P., Kendall B.J., Pandeya N., Whiteman D.C. A model to determine absolute risk for esophageal adenocarcinoma. Clin. Gastroenterol. Hepatol. 2013, 11. 138-144.e2.
37. Hu X., Cammann H., Meyer H.-A., Miller K., Jung K., Stephan C. Artificial neural networks and prostate cancer-tools for diagnosis and management. Nat. Rev. Urol. 2013, 10:174-182.
38. Pegolo S., Gallina G., Montesissa C., Capolongo F., Ferraresso S., Pellizzari C., Poppi L., Castagnaro M., Bargelloni L. Transcriptomic markers meet the real world: finding diagnostic signatures of corticosteroid treatment in commercial beef samples. BMC Vet. Res. 2012, 8:205.
39. Akanuma H., Qin X.Y., Nagano R., Win-Shwe T.T., Imanishi S., Zaha H., Yoshinaga J., Fukuda T., Ohsako S., Sone H. Identification of stage-specific gene expression signatures in response to retinoic acid during the neural differentiation of mouse embryonic stem cells. Front. Genet. 2012, 3:141.
40. Dennis G., Sherman B.T., Hosack D.A., Yang J., Gao W., Lane H.C., Lempicki R.A. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003, 4:P3.
41. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 1995, 57:289-300.
42. Globe D., Bayliss M.S., Harrison D.J. The impact of itch symptoms in psoriasis: results from physician interviews and patient focus groups. Health Qual. Life Outcomes 2009, 7:62.
43. Boy M.G., Wang C., Wilkinson B.E., Chow V.F., Clucas A.T., Krueger J.G., Gaweco A.S., Zwillich S.H., Changelian P.S., Chan G. Double-blind, placebo-controlled, dose-escalation study to evaluate the pharmacologic effect of CP-690,550 in patients with psoriasis. J. Invest. Dermatol. 2009, 129:2299-2302.
44. Guttman-Yassky E., Suarez-Farinas M., Chiricozzi A., Nograles K.E., Shemer A., Fuentes-Duculan J., Cardinale I., Lin P., Bergman R., Bowcock A.M., Krueger J.G. Broad defects in epidermal cornification in atopic dermatitis identified through genomic analysis. J. Allergy Clin. Immunol. 2009, 124:1235-1244. (e1258).
45. Bergboer J.G., Zeeuwen P.L., Schalkwijk J. Genetics of psoriasis: evidence for epistatic interaction between skin barrier abnormalities and immune deviation. J. Invest. Dermatol. 2012, 132:2320-2321.
46. Bergboer J.G., Zeeuwen P.L., Schalkwijk J. Genetics of psoriasis: evidence for epistatic interaction between skin barrier abnormalities and immune deviation. J. Invest. Dermatol. 2013, 132:2320-2331.
47. Madonna S., Scarponi C., Pallotta S., Cavani A., Albanesi C. Anti-apoptotic effects of suppressor of cytokine signaling 3 and 1 in psoriasis. Cell Death Dis. 2012, 3:e334.
48. Pasparakis M. Role of NF-kappaB in epithelial biology. Immunol. Rev. 2012, 246:346-358.
49. Krulig E., Gordon K.B. Ustekinumab: an evidence-based review of its effectiveness in the treatment of psoriasis. Core Evid. 2010, 5:11-22.
50. Roberson E.D., Liu Y., Ryan C., Joyce C.E., Duan S., Cao L., Martin A., Liao W., Menter A., Bowcock A.M. A subset of methylated CpG sites differentiate psoriatic from normal skin. J. Invest. Dermatol. 2012, 132:583-592.
51. Lobito A.A., Ramani S.R., Tom I., Bazan J.F., Luis E., Fairbrother W.J., Ouyang W., Gonzalez L.C. Murine insulin growth factor-like (IGFL) and human IGFL1 proteins are induced in inflammatory skin conditions and bind to a novel tumor necrosis factor receptor family member, IGFLR1. J. Biol. Chem. 2011, 286:18969-18981.
52. Emtage P., Vatta P., Arterburn M., Muller M.W., Park E., Boyle B., Hazell S., Polizotto R., Funk W.D., Tang Y.T. IGFL: a secreted family with conserved cysteine residues and similarities to the IGF superfamily. Genomics 2006, 88:513-520.
53. Jones S.M., Kazlauskas A. Growth-factor-dependent mitogenesis requires two distinct phases of signalling. Nat. Cell Biol. 2001, 3:165-172.
54. Fukushima T., Nakamura Y., Yamanaka D., Shibano T., Chida K., Minami S., Asano T., Hakuno F., Takahashi S. Phosphatidylinositol 3-kinase (PI3K) activity bound to insulin-like growth factor-I (IGF-I) receptor, which is continuously sustained by IGF-I stimulation, is required for IGF-I-induced cell proliferation. J. Biol. Chem. 2012, 287:29713-29721.
55. Magrane M., Consortium U. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011, 2011:bar009.
56. Ponten F., Schwenk J.M., Asplund A., Edqvist P.H. The Human Protein Atlas as a proteomic resource for biomarker discovery. J. Intern. Med. 2011, 270:428-446.
57. Roy A., Kucukural A., Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 2010, 5:725-738.
58. Zhang Y., Skolnick J. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys. J. 2004, 87:2647-2655.
59. Zheng H., Worrall C., Shen H., Issad T., Seregard S., Girnita A., Girnita L. Selective recruitment of G protein-coupled receptor kinases (GRKs) controls signaling of the insulin-like growth factor 1 receptor. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:7055-7060.
60. Ogihara T., Isobe T., Ichimura T., Taoka M., Funaki M., Sakoda H., Onishi Y., Inukai K., Anai M., Fukushima Y., Kikuchi M., Yazaki Y., Oka Y., Asano T. 14-3-3 protein binds to insulin receptor substrate-1, one of the binding sites of which is in the phosphotyrosine binding domain. J. Biol. Chem. 1997, 272:25267-25274.
61. Benomar Y., Roy A.F., Aubourg A., Djiane J., Taouis M. Cross down-regulation of leptin and insulin receptor expression and signalling in a human neuronal cell line. Biochem. J. 2005, 388:929-939.
62. Liu Y. Identification of Genetic and Epigenetic Risk Factors for Psoriasis and Psoriatic Arthritis in: Graduate School of Arts and Sciences 2011, 193. Washington University in St. Louis, St. Louis, MO.
63. Chu S.H., Feng D.F., Ma Y.B., Zhang H., Zhu Z.A., Li Z.Q., Jiang P.C. Promoter methylation and downregulation of SLC22A18 are associated with the development and progression of human glioma. J. Transl. Med. 2011, 9:156.