title: New insights about host response to smallpox using microarray data.
abstract: BACKGROUND
  Smallpox is a lethal disease that was endemic in many parts of the world until eradicated by massive immunization. Due to its lethality, there are serious concerns about its use as a bioweapon. Here we analyze publicly available microarray data to further understand survival of smallpox infected macaques, using systems biology approaches. Our goal is to improve the knowledge about the progression of this disease.
  
  
  RESULTS
  We used KEGG pathways annotations to define groups of genes (or modules), and subsequently compared them to macaque survival times. This technique provided additional insights about the host response to this disease, such as increased expression of the cytokines and ECM receptors in the individuals with higher survival times. These results could indicate that these gene groups could influence an effective response from the host to smallpox.
  
  
  CONCLUSIONS
  Macaques with higher survival times clearly express some specific pathways previously unidentified using regular gene-by-gene approaches. Our work also shows how third party analysis of public datasets can be important to support new hypotheses to relevant biological problems.
authors: BIOINFO, Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil. gesteves@vision.ime.usp.br
authors: Gustavo H
authors: GH
authors: Esteves
authors: Ana C Q
authors: AC
authors: Simoes
authors: Estevao
authors: E
authors: Souza
authors: Rodrigo A
authors: RA
authors: Dias
authors: Raydonal
authors: R
authors: Ospina
authors: Thiago M
authors: TM
authors: Venancio
mesh_terms: D000818:Animals; D015815:Cell Adhesion Molecules / Q000235:genetics; D003198:Computer Simulation; D016207:Cytokines / Q000235:genetics; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D007694:Killer Cells, Natural / Q000276:immunology; D008251:Macaca / Q000235:genetics* / Q000821:virology*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D012899:Smallpox / Q000235:genetics* / Q000276:immunology / Q000401:mortality / Q000821:virology; D015996:Survival Rate; D049490:Systems Biology
chemical_list: D015815:Cell Adhesion Molecules; D016207:Cytokines
references: Nature. 2000 Feb 3;403(6769):503-11
references: 10676951
references: Immunol Rev. 2006 Dec;214:239-50
references: 17100889
references: Nucleic Acids Res. 2001 Jan 1;29(1):152-5
references: 11125075
references: Nucleic Acids Res. 2002 Jan 1;30(1):42-6
references: 11752249
references: Immunity. 2002 Jan;16(1):51-65
references: 11825565
references: Nat Rev Immunol. 2001 Oct;1(1):41-9
references: 11905813
references: Virus Res. 2002 Sep;88(1-2):35-53
references: 12297326
references: N Engl J Med. 2003 Jan 30;348(5):416-25
references: 12496353
references: Annu Rev Immunol. 2003;21:377-423
references: 12543935
references: Genome Biol. 2004;5(8):R60
references: 15287982
references: Nat Genet. 2004 Oct;36(10):1090-8
references: 15448693
references: Proc Natl Acad Sci U S A. 2004 Oct 19;101(42):15196-200
references: 15477589
references: Proc Natl Acad Sci U S A. 2004 Oct 19;101(42):15190-5
references: 15477590
references: Immunity. 1998 Apr;8(4):473-82
references: 9586637
references: Cell. 1999 Mar 19;96(6):857-68
references: 10102273
references: JAMA. 1999 Jun 9;281(22):2127-37
references: 10367824
references: Nature. 2005 Sep 15;437(7057):426-31
references: 16163360
references: Nat Med. 2006 Nov;12(11):1310-5
references: 17086190
references: Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12182-6
references: 11027309