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Review

Merging experimental data and in silico analysis: a systems-level approach to autoimmune disease and cancer

Pages 361-372 | Published online: 10 Jan 2014

References

  • Lin PI, Vance JM, Pericak-Vance MA, Martin ER. No gene is an island: the flip-flop phenomenon. Am. J. Hum. Genet.80(3), 531–538 (2007).
  • Tramontano A. No protein is an island. Curr. Opin. Struct. Biol.19(3), 310–311 (2009).
  • Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet.2, 343–372 (2001).
  • Ingolia NT, Weissman JS. Systems biology: reverse engineering the cell. Nature454(7208), 1059–1062 (2008).
  • Bourret RB. Signal transduction meets systems biology: deciphering specificity determinants for PPIs. Mol. Microbiol.69(6), 1336–1340 (2008).
  • Bruggeman FJ, Westerhoff HV. The nature of systems biology. Trends Microbiol.15, 45–50 (2007).
  • Preisinger C, von Kriegsheim A, Matallanas D, Kolch W. Proteomics and phosphoproteomics for the mapping of cellular signalling networks. Proteomics8(21), 4402–4415 (2008).
  • Ramaswamy S, Ross KN, Lander ES, Golub TR. A molecular signature of metastasis in primary solid tumors. Nat. Genet.33, 49–54 (2003).
  • Ramaswamy S. Rational design of cancer-drug combinations. N. Engl. J. Med.357, 299–300 (2007).
  • Baechler EC, Batliwalla FM, Karypis G et al. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc. Natl Acad. Sci. USA100, 2610–2615 (2003).
  • Weigelt B, Hu Z, He X et al. Molecular portraits and 70-gene prognosis signature are preserved throughout the metastatic process of breast cancer. Cancer Res.65(20), 9155–9158 (2005).
  • Cirillo N, Prime SS. Desmosomal interactome in keratinocytes: a systems biology approach leading to an understanding of the pathogenesis of skin disease. Cell. Mol. Life Sci.66(21), 3517–3533 (2009).
  • Lim KP, Cirillo N, Hassona Y et al. Fibroblast gene expression profile reflects the stage of tumour progression in oral squamous cell carcinoma. J. Pathol.223(4), 459–469 (2011).
  • Hess EL. Origins of molecular biology. Science168, 664–669 (1970).
  • Strange K. The end of “naive reductionism”: rise of systems biology or renaissance of physiology? Am. J. Physiol. Cell Physiol.288(5), C968–C974 (2005).
  • Bloom FE. What does it all mean to you? J. Neurosci.21, 8304–8305 (2001).
  • Kitano H. Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology. Curr. Genet.41, 1–10 (2002).
  • Kitano H. Systems biology: a brief overview. Science295, 1662–1664 (2002).
  • Bader GD, Hogue CW. Analyzing yeast PPI data obtained from different sources. Nat. Biotechnol.20, 991–997 (2002).
  • Zaidel-Bar R, Itzkovitz S, Ma’ayan A, Iyengar R, Geiger B. Functional atlas of the integrin adhesome. Nat. Cell Biol.9, 858–867 (2007).
  • Dyer MD, Murali TM, Sobral BW. Computational prediction of host-pathogen PPIs. Bioinformatics23(13), I159–I166 (2007).
  • Pieroni E, de la Fuente van Bentem S, Mancosu G, Capobianco E, Hirt H, de la Fuente A. Protein networking: insights into global functional organization of proteomes. Proteomics8(4), 799–816 (2008).
  • Paschoal PO, Chamberlin W. Review of the 1st Annual World Congress of Immunodiseases and Therapeutics. Expert Rev. Clin. Immunol.6(5), 757–759 (2010).
  • Schöner D, Barkow S, Bleuler S et al. Network analysis of systems elements. EXS97, 331–351 (2007).
  • Geier F, Timmer J, Fleck C. Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. BMC Syst. Biol.1, 11 (2007).
  • Kumar A, Snyder M. Proteomics: protein complexes take the bait. Nature415, 123–124 (2002).
  • Virtanen C, Woodgett J. Clinical uses of microarrays in cancer research. Methods Mol. Med.141, 87–113 (2008).
  • Leung YF, Cavalieri D. Fundamentals of cDNA microarray data analysis. Trends Genet.19, 649–659 (2003).
  • Quackenbush J. Computational analysis of microarray data. Nat. Rev. Genet.2, 418–427 (2001).
  • Slonim DK. From patterns to pathways: gene expression data analysis comes of age. Nat. Genet.32(Suppl.), 502–508 (2002).
  • Zaravinos A, Lambrou GI, Boulalas I, Delakas D, Spandidos DA. Identification of common differentially expressed genes in urinary bladder cancer. PLoS ONE6(4), E18135 (2011).
  • Mendes A, Scott RJ, Moscato P. Microarrays – identifying molecular portraits for prostate tumors with different Gleason patterns. Methods Mol. Med.141, 131–151 (2008).
  • Sikaroodi M, Galachiantz Y, Baranova A. Tumor markers: the potential of “omics” approach. Curr. Mol. Med.10(2), 249–257 (2010).
  • Zaidel-Bar R, Geiger B. The switchable integrin adhesome. J. Cell. Sci.123(9), 1385–1388 (2010).
  • Said MR, Begley TJ, Oppenheim AV, Lauffenburger DA, Samson LD. Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc. Natl Acad. Sci.101, 18006–18011 (2004).
  • Vallabhajosyula RR, Raval A. Computational modeling in systems biology. Methods Mol. Biol.662, 97–120 (2010).
  • Efroni S, Schaefer CF, Buetow KH. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS ONE2(5), E425 (2007).
  • Wachi S, Yoneda K, Wu R. Interactome–transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics21, 4205–4208 (2005).
  • Kyttaris VC, Krishnan S, Tsokos GC. Systems biology in systemic lupus erythematosus: integrating genes, biology and immune function. Autoimmunity39(8), 705–709 (2006).
  • Tuller T, Atar S, Ruppin E, Gurevich M, Achiron A. Global map of physical interactions among differentially expressed genes in multiple sclerosis relapses and remissions. Hum. Mol. Genet.20(18), 3606–3619 (2011).
  • Ideker T, Sharan R. Protein networks in disease. Genome Res.18(4), 644–652 (2008).
  • Matthews LR, Vaglio P, Reboul J et al. Identification of potential interaction networks using sequence-based searches for conserved PPIs or “interologs.” Genome Res.11, 2120–2126 (2001).
  • Jonsson PF, Bates PA. Global topological features of cancer proteins in the human interactome. Bioinformatics22, 2291–2297 (2006).
  • Futreal PA, Coin L, Marshall M et al. A census of human cancer genes. Nat. Rev. Cancer4, 177–183 (2004).
  • Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabasi AL. The human disease network. Proc. Natl Acad. Sci. USA104, 8685–8690 (2007).
  • Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledge base of human genes and genetic disorders. Nucleic Acids Res.33, D514–D517 (2005).
  • Harris MA, Clark J, Ireland A et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res.32, D258–D261 (2004).
  • Calvano SE, Xiao W, Richards DR et al. A network-based analysis of systemic inflammation in humans. Nature437, 1032–1037 (2005).
  • Amagai M, Klaus-Kovtun V, Stanley JR. Autoantibodies against a novel epithelial cadherin in pemphigus vulgaris, a disease of cell adhesion. Cell67, 869–877 (1991).
  • Payne AS, Hanakawa Y, Amagai M, Stanley JR. Desmosomes and disease: pemphigus and bullous impetigo. Curr. Opin. Cell Biol.16, 536–543 (2004).
  • Bystryn JC, Rudolph JL. Pemphigus. Lancet366, 61–73 (2005).
  • Cirillo N. Pathophysiology of the desmosome. Research Signpost, Kerala, India (2009).
  • Waschke J. The desmosome and pemphigus. Histochem. Cell. Biol.130, 21–54 (2008).
  • Amagai M, Karpati S, Prussick R, Klaus-Kovtun V, Stanley JR. Autoantibodies against the amino-terminal cadherin-like binding domain of pemphigus vulgaris antigen are pathogenic. J. Clin. Invest.90, 919–926 (1992).
  • Nguyen VT, Ndoye A, Grando SA. Novel human 9 acetylcholine receptor regulating keratinocyte adhesion is targeted by pemphigus vulgaris autoimmunity. Am. J. Pathol.157, 1377–1391 (2000).
  • Nguyen VA, Ndoye A, Grando SA. Pemphigus vulgaris antibody identifies pemphaxin, a novel keratinocyte annexin-like molecule binding acetylcholine. J. Biol. Chem.275, 29466–29476 (2000).
  • Lanza A, Cirillo N, Femiano F, Gombos F. How does acantholysis occur in pemphigus vulgaris: a critical review. J. Cutan. Pathol.33, 401–412 (2006).
  • Shannon P, Markiel A, Ozier O et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res.13, 2498–2504 (2003).
  • Albert R, Jeong H, Barabasi AL. Error and attack tolerance of complex networks. Nature406, 378–382 (2000).
  • Lanza A, Cirillo N, Rossiello R et al. Evidence of key role of Cdk2 overexpression in pemphigus vulgaris. J. Biol. Chem.283, 8736–8745 (2008).
  • Palacios R, Goni J, Martinez-Forero I et al. A network analysis of the human T-cell activation gene network identifies JAGGED1 as a therapeutic target for autoimmune diseases. PLoS ONE21, E1222 (2007).
  • Ptitsyn AA, Weil MM, Thamm DH. Systems biology approach to identification of biomarkers for metastatic progression in cancer. BMC Bioinformatics9(Suppl. 9), S8 (2008).
  • Thurlow JK, Peña Murillo CL, Hunter KD et al. Spectral clustering of microarray data elucidates the roles of microenvironment remodeling and immune responses in survival of head and neck squamous cell carcinoma. J. Clin. Oncol.28(17), 2881–2888 (2010).
  • Chung CH, Parker JS, Karaca G et al. Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell5, 489–500 (2004).
  • Przytycka TM, Kim YA. Network integration meets network dynamics. BMC Biol.8, 48 (2010).

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