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Unsupervised analysis of follicular thyroid tumours transcriptome by oligonucleotide microarray gene expression profiling
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Abstract
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.
Material and 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. (Endokrynol Pol 2013; 64 (5): 328–334)
Abstract
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.
Material and 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. (Endokrynol Pol 2013; 64 (5): 328–334)
Keywords
follicular thyroid carcinoma; follicular adenoma; gene expression
About this articleTitle
Unsupervised analysis of follicular thyroid tumours transcriptome by oligonucleotide microarray gene expression profiling
Journal
Issue
Article type
Original paper
Pages
328-334
Published online
2013-11-01
Page views
1820
Article views/downloads
1776
DOI
10.5603/EP.2013.0013
Bibliographic record
Endokrynol Pol 2013;64(5):328-334.
Keywords
follicular thyroid carcinoma
follicular adenoma
gene expression
Authors
Bartosz Wojtaś
Aleksandra Pfeifer
Michał Jarząb
Agnieszka Czarniecka
Jolanta Krajewska
Michał Świerniak
Tomasz Stokowy
Dagmara Rusinek
Monika Kowal
Jadwiga Żebracka-Gala
Tomasz Tyszkiewicz
Małgorzata Oczko-Wojciechowska
Ewa Stobiecka
Dariusz Lange
Ralf Paschke
Barbara Jarząb
