title: Gene expression is highly correlated on the chromosome level in urinary bladder cancer.
abstract: OBJECTIVE
  Chromosome correlation maps display correlations between gene expression patterns on the same chromosome. Our goal was to map the genes on chromosome regions and to identify correlations through their location on chromosome regions.
  
  
  METHODS
  Following microarray analysis we used Ingenuity Pathway Analysis (IPA) to construct gene networks of the co-deregulated genes in bladder cancer. Chromosome mapping, mathematical modeling and data simulations were performed using the WebGestalt and Matlab(®) softwares.
  
  
  RESULTS
  The top deregulated molecules among 129 bladder cancer samples were implicated in the PI3K/AKT signaling, cell cycle, Myc-mediated apoptosis signaling and ERK5 signaling pathways. Their most prominent molecular and cellular functions were related to cell cycle, cell death, gene expression, molecular transport and cellular growth and proliferation. Chromosome correlation maps allowed us to detect significantly co-expressed genes along the chromosomes. We identified strong correlations among tumors of Tα-grade 1, as well as for those of Tα-grade 2, in chromosomes 1, 2, 3, 7, 12 and 19. Chromosomal domains of gene co-expression were revealed for the normal tissues, as well. The expression data were further simulated, exhibiting an excellent fit (0.7 < R(2) < 0.9). The simulations revealed that along the different samples, genes on same chromosomes are expressed in a similar manner.
  
  
  CONCLUSIONS
  Gene expression is highly correlated on the chromosome level. Chromosome correlation maps of gene expression signatures can provide further information on gene regulatory mechanisms. Gene expression data can be simulated using polynomial functions.
authors.affiliation: First Department of Pediatrics, University of Athens, Choremeio Research Laboratory, Athens, Greece.
authors.forename: George I
authors.initials: GI
authors.lastname: Lambrou
authors.forename: Maria
authors.initials: M
authors.lastname: Adamaki
authors.forename: Dimitris
authors.initials: D
authors.lastname: Delakas
authors.forename: Demetrios A
authors.initials: DA
authors.lastname: Spandidos
authors.forename: Spyros
authors.initials: S
authors.lastname: Vlahopoulos
authors.forename: Apostolos
authors.initials: A
authors.lastname: Zaravinos
mesh_terms: D000465:Algorithms; D002877:Chromosomes, Human / Q000378:metabolism*; D015331:Cohort Studies; D030541:Databases, Genetic; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D060787:Neoplasm Grading; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction / Q000235:genetics; D001749:Urinary Bladder Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology
keywords: bladder cancer; chromosome correlation maps; data simulations; mathematical modeling; molecular networks