title: Gene clustering analysis in human osteoporosis disease and modifications of the jawbone.
abstract: OBJECTIVE
  An analysis of the genes involved in both osteoporosis and modifications of the jawbone, through text mining, using a web search tool, of information regarding gene/protein interaction.
  
  
  METHODS
  The final set of genes involved in the present phenomenon was obtained by expansion-filtering loop. Using a web-available software (STRING), interactions among all genes were searched for, and a clustering procedure was performed in which only high-confidence predicted associations were considered.
  
  
  RESULTS
  Two hundred forty-two genes potentially involved in osteoporosis and in modifications of the jawbone were recorded. Seven "leader genes" were identified (CTNNB1, IL1B, IL6, JUN, RUNX2, SPP1, TGFB1), while another 10 genes formed the cluster B group (BMP2, BMP7, COL1A1, ICAM1, IGF1, IL10, MMP9, NFKB1, TNFSF11, VEGFA). Ninety-eight genes had no interactions, and were defined as "orphan genes".
  
  
  CONCLUSIONS
  The expansion of knowledge regarding the molecular basis causing osteoporotic traits has been brought about with the help of a de novo identification, based on the data mining of genes involved in osteoporosis and in modification of the jawbone. A comparison of the present data, in which no role was verified for 98 genes that had been previously supposed to have a role, with that of the literature, in which another 81 genes, as obtained from GWAS reviews and meta-analyses, appeared to be strongly associated with osteoporosis, probably attests to a lack of information on osteoporotic disease.
authors.affiliation: Private Practice, Via Provinciale 87B, 55041 Camaiore Lucca, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Toti
authors.forename: Carolina
authors.initials: C
authors.lastname: Sbordone
authors.forename: Ranieri
authors.initials: R
authors.lastname: Martuscelli
authors.forename: Luigi
authors.initials: L
authors.lastname: Califano
authors.forename: Luca
authors.initials: L
authors.lastname: Ramaglia
authors.forename: Ludovico
authors.initials: L
authors.lastname: Sbordone
mesh_terms: D055396:Bone Morphogenetic Protein 2 / Q000235:genetics; D055419:Bone Morphogenetic Protein 7 / Q000235:genetics; D001861:Bone Regeneration / Q000235:genetics; D016723:Bone Remodeling / Q000235:genetics; D001862:Bone Resorption / Q000235:genetics; D024042:Collagen Type I / Q000235:genetics; D000090602:Collagen Type I, alpha 1 Chain; D019295:Computational Biology; D050659:Core Binding Factor Alpha 1 Subunit / Q000235:genetics; D057225:Data Mining; D016758:Genes, jun / Q000235:genetics; D006801:Humans; D007334:Insulin-Like Growth Factor I / Q000235:genetics; D018799:Intercellular Adhesion Molecule-1 / Q000235:genetics; D016753:Interleukin-10 / Q000235:genetics; D053583:Interleukin-1beta / Q000235:genetics; D015850:Interleukin-6 / Q000235:genetics; D007571:Jaw Diseases / Q000235:genetics*; D020780:Matrix Metalloproteinase 9 / Q000235:genetics; D005810:Multigene Family / Q000235:genetics*; D052002:NF-kappa B p50 Subunit / Q000235:genetics; D053495:Osteopontin / Q000235:genetics; D010024:Osteoporosis / Q000235:genetics*; D053245:RANK Ligand / Q000235:genetics; D053773:Transforming Growth Factor beta1 / Q000235:genetics; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics; D051176:beta Catenin / Q000235:genetics
chemical_list: C525718:BMP2 protein, human; C525819:BMP7 protein, human; D055396:Bone Morphogenetic Protein 2; D055419:Bone Morphogenetic Protein 7; C495270:CTNNB1 protein, human; D024042:Collagen Type I; D000090602:Collagen Type I, alpha 1 Chain; D050659:Core Binding Factor Alpha 1 Subunit; C573420:ICAM1 protein, human; D053583:Interleukin-1beta; D015850:Interleukin-6; D052002:NF-kappa B p50 Subunit; C489548:NFKB1 protein, human; D053245:RANK Ligand; C493709:RUNX2 protein, human; C506895:SPP1 protein, human; C505688:TNFSF11 protein, human; D053773:Transforming Growth Factor beta1; C467484:VEGFA protein, human; D042461:Vascular Endothelial Growth Factor A; D051176:beta Catenin; D053495:Osteopontin; D018799:Intercellular Adhesion Molecule-1; D016753:Interleukin-10; D007334:Insulin-Like Growth Factor I; C579270:MMP9 protein, human; D020780:Matrix Metalloproteinase 9