Expression profiling identifies genes involved in emphysema severity

doi:10.1186/1465-9921-10-81

Respiratory Research

Volume 10

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Expression profiling identifies genes involved in emphysema severity

Santiyagu M Savarimuthu Francis¹^,2 , Jill E Larsen¹^,2 , Sandra J Pavey² , Rayleen V Bowman¹^,2 , Nicholas K Hayward²^,3 , Kwun M Fong¹^,2 and Ian A Yang¹^,2

¹Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia

²School of Medicine, The University of Queensland, Brisbane, Australia

³Department of human genetics, Oncogenomics Laboratory, Queensland Institute of Medical Research, Brisbane, Australia

author email corresponding author email

Respiratory Research 2009, 10:81doi:10.1186/1465-9921-10-81


Published:	2 September 2009

Additional files

Additional file 1:

Primer sequences of genes chosen for technical and biological validation. List of primer sequences used in the validation of microarray probes using qRt-PCR

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Additional file 2:

Table of 91 genes identified using class comparison analysis. Genes differentially expressed between mild and moderate emphysema patients. "Y" indicates that the probes have been represented in Affymetrix HG-U133A microarray chip.

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Additional file 3:

Comparison of class prediction analysis of 51 genes in public datasets. Class prediction results of 51 genes in TPCH training, Spira and Golpon dataset using Nearest Centroid Correct algorithm. "YES" indicates that the sample has been classified correctly and "NO" indicates that the sample has been classified incorrectly.

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Additional file 4:

Dendrogram of shortlisted 51 genes. Supervised two-dimensional hierarchical clustering based on average linkage uncentered correlation of emphysema samples using microarray expression data of the 51 genes represented in Spira and Golpon platforms chosen for qRT-PCR validation on TPCH training set. Each column represents a sample and each row represents a gene. Mild emphysema samples are indicated by the blue bar and moderate emphysema samples are indicated by the orange bar. Heatmap indicates level of gene expression, red, high expression, green, low expression in moderate compared to mild emphysema severity.

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Additional file 5:

Comparison of class prediction analysis of 7 candidate genes in public datasets. Class prediction results of 7 genes in TPCH test, Spira and Golpon dataset using Nearest Centroid Correct algorithm. "YES" indicates that the sample has been classified correctly and "NO" indicates that the sample has been classified incorrectly.

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Additional file 6:

Pathway analysis on candidate genes. Canonical Pathway analysis in IPA on the seven validated candidate genes. The most significant functional and canonical groups, with p < 0.05 are presented. The bars represent p-value in logarithmic scale for each functional or canonical group and genes assigned to each of the functions are listed.

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Additional file 7:

Over-representation of gene ontologies in candidate genes. Heatmap (a) and enrichment score (b) of gene ontologies overrepresented in six of the seven candidates. a) Represents common gene ontologies enriched in the candidate genes. b) Significant clustering (Fisher's Exact, p < 0.05) of molecular, biological and cellular functions in the candidate genes.

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