Altered expression of mitochondrial and extracellular matrix genes in the heart of human fetuses with chromosome 21 trisomy

Additional file 1:

Genes expressed in human fetal heart at 18–22 weeks of gestation. Genes are reported if the Affymetrix presence call was 'Present' in at least 10 heart samples. Genes are sorted by alphabetical order.

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Additional file 2:

Hsa21 genes expressed in the human fetal heart at 18–22 weeks of gestation. Genes (probe sets) are sorted according to chromosomal location. Mitochondrial and ECM genes are in bold.

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Additional file 3:

Scatter plot of gene expression data of trisomic samples vs. control samples. Mean raw, log transformed, gene expression data from the 5 control samples (NH) were plotted on the x-axis and data from the 10 trisomic samples (DSH) were plotted on the y-axis. Plots are shown for Hsa21 genes and for genes of all chromosomes excluding Hsa21. In the plot of Hsa21 more than 75% of gene probe sets are above the line, whereas in the plot of all other chromosomes approximately the same number of gene probe sets is above and below the line. Abbreviations for DSH and NH are as in Figure 1.

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Additional file 4:

Genes differentially expressed between trisomic and control samples. The table includes genes with fold change > |1.2| and p < 0.05 (ANOVA test). Genes are sorted according to fold change.

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Additional file 5:

List of downregulated genes encoding mitochondrial proteins, and of upregulated genes encoding extracellular matrix proteins. Hsa21 genes are in bold.

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Additional file 6:

Genes differentially expressed between trisomic and control samples using gc-RMA preprocessed data. The table includes genes with fold change > |1.2| and p < 0.05 (ANOVA test). Genes are sorted according to fold change. Hsa21 genes are in bold.

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Additional file 7:

Enrichment score plots of the five biologically informative sets correlated to the DS condition with an FDR value < 0.05. Extracellular matrix and Cell adhesion gene sets are positively correlated to DS condition whereas Mitochondria, Electron transport chain and Oxidative phosphorylation gene sets are negatively correlated. The enrichment score (ES) represents the degree to which a gene set is enriched at the top (positive ES) or at the bottom (negative ES) of our ranked list. The size indicated for each gene set is the dimension of the leading edge subset that is the subset of members of our list that contribute more to the enrichment score (ES). The nominal p-value and the False Discovery Rate (FDR) value estimate the probability that the enrichment score represents a false positive finding.

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Additional file 8:

Condition tree generated using the hierarchical clustering approach. The tree groups samples together based on the similarity of their expression data across a gene list including ~1000 genes, not mapping to Hsa21, which encode mitochondrial and ECM proteins. The 15 DS samples are clustered together on the left whereas the five control samples are clustered on the right of the image demonstrating that the expression of genes in the specified list can be used to correctly separate DSH from NH samples.

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