title: Meta-data analysis as a strategy to evaluate individual and common features of proteomic changes in breast cancer.
abstract: BACKGROUND
  Individual differences among breast tumours in patients is a significant challenge for the treatment of breast cancer. This study reports a strategy to assess these individual differences and the common regulatory mechanisms that may underlie breast tumourigenesis.
  
  
  METHODS
  The two-step strategy was based firstly on a full-scale proteomics analysis of individual cases, and secondly on the analysis of common features of the individual proteome-centred networks (meta-data).
  
  
  RESULTS
  Proteomic profiling of human invasive ductal carcinoma tumours was performed and each case was analysed individually. Analysis of primary datasets for common cancer-related proteins identified keratins. Analysis of individual networks built with identified proteins predicted features and regulatory mechanisms involved in each individual case. Validation of these findings by immunohistochemistry confirmed the predicted deregulation of expression of CK2α, PDGFRα, PYK and p53 proteins.
  
  
  CONCLUSIONS
  Meta-data analysis allowed efficient evaluation of both individual and common features of the breast cancer proteome.
authors.affiliation: Department of Oncology-Pathology, Karolinska Biomics Center, Karolinska Institute, Stockholm, Sweden.
authors.forename: Olena
authors.initials: O
authors.lastname: Zakharchenko
authors.forename: Christina
authors.initials: C
authors.lastname: Greenwood
authors.forename: Anna
authors.initials: A
authors.lastname: Lewandowska
authors.forename: Ulf
authors.initials: U
authors.lastname: Hellman
authors.forename: Louise
authors.initials: L
authors.lastname: Alldridge
authors.forename: Serhiy
authors.initials: S
authors.lastname: Souchelnytskyi
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D044584:Carcinoma, Ductal / Q000235:genetics* / Q000473:pathology; D015536:Down-Regulation; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007150:Immunohistochemistry; D053858:Metabolic Networks and Pathways / Q000235:genetics; D009361:Neoplasm Invasiveness; D040901:Proteomics; D020796:Receptor, Platelet-Derived Growth Factor alpha / Q000235:genetics; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D015854:Up-Regulation
chemical_list: D014408:Biomarkers, Tumor; D016159:Tumor Suppressor Protein p53; D020796:Receptor, Platelet-Derived Growth Factor alpha