title: Unsupervised analysis of follicular thyroid tumours transcriptome by oligonucleotide microarray gene expression profiling.
abstract: BACKGROUND
  Mechanisms driving the invasiveness of follicular thyroid cancer (FTC) are not fully understood. In our study, we undertook an unsupervised analysis of the set of follicular thyroid tumours (adenomas (FTA) and carcinomas) to verify whether the malignant phenotype influences major sources of variability in our dataset.
  
  
  METHODS
  The core set of samples consisted of 52 tumours (27 FTC, 25 FTA). Total RNA was analysed by oligonucleotide microarray (HG-U133 Plus 2.0). Principal Component Analysis (PCA) was applied as a main method of unsupervised analysis.
  
  
  RESULTS
  An analysis of biological character of genes correlated to the first six PCs was performed. When genes correlated to the first PC were used to cluster FTC and FTA, they appeared in two branches; one, relatively enriched in adenomas, with homogenous expression of subset of genes, and the other containing mainly carcinomas, with down-regulation of these genes and heterogeneous up-regulation in a smaller cluster of transcripts. Genes highly up-regulated in adenomas included some thyroid-specific transcripts. The second cluster of genes, up-regulated in carcinomas, contained mainly immunity-related transcripts. Immune response genes were found in the first, third and sixth principal components, improving the discrimination between carcinomas and adenomas.
  
  
  CONCLUSIONS
  Our unsupervised analysis indicates that invasiveness of follicular tumours might be considered as the major source of variability in transcriptome analysis. However, the distance between both groups is small and the clusters are overlapping, thus, unsupervised analysis is not sufficient to properly classify them.
authors.affiliation: bjarzab@io.gliwice.pl.
authors.forename: Bartosz
authors.initials: B
authors.lastname: Wojtaś
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Pfeifer
authors.forename: Michał
authors.initials: M
authors.lastname: Jarząb
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Czarniecka
authors.forename: Jolanta
authors.initials: J
authors.lastname: Krajewska
authors.forename: Michał
authors.initials: M
authors.lastname: Swierniak
authors.forename: Tomasz
authors.initials: T
authors.lastname: Stokowy
authors.forename: Dagmara
authors.initials: D
authors.lastname: Rusinek
authors.forename: Monika
authors.initials: M
authors.lastname: Kowal
authors.forename: Jadwiga
authors.initials: J
authors.lastname: Zebracka-Gala
authors.forename: Tomasz
authors.initials: T
authors.lastname: Tyszkiewicz
authors.forename: Małgorzata
authors.initials: M
authors.lastname: Oczko-Wojciechowska
authors.forename: Ewa
authors.initials: E
authors.lastname: Stobiecka
authors.forename: Dariusz
authors.initials: D
authors.lastname: Lange
authors.forename: Ralf
authors.initials: R
authors.lastname: Paschke
authors.forename: Barbara
authors.initials: B
authors.lastname: Jarząb
mesh_terms: D018263:Adenocarcinoma, Follicular / Q000145:classification / Q000235:genetics* / Q000473:pathology*; D002453:Cell Cycle / Q000235:genetics; D003937:Diagnosis, Differential; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D009361:Neoplasm Invasiveness; D020411:Oligonucleotide Array Sequence Analysis; D025341:Principal Component Analysis; D013964:Thyroid Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology*; D059467:Transcriptome