Journal: JCI Insight

Article Title: Transcriptomics and machine learning predict diagnosis and severity of growth hormone deficiency

doi: 10.1172/jci.insight.93247

Figure Lengend Snippet: (A) Heatmap for the probe sets identified by correlation with peak GH (347 probe sets, 271 unique genes). Five distinct clusters of gene expression are identified via the dendrogram — two positively correlated (red) with peak GH and three negatively correlated (green). Pink, yellow, and blue squares indicate the principal component analysis group for each patient (see Figure 1B). (B) Isomap supervised principal component analysis using only those probe sets whose expression correlated to peak GH identified 3 distinct groups of GHD subjects (n = 98; pink n = 49, yellow n = 37, and blue n = 12).

Article Snippet: Dimensional scaling using PCA and isomap multidimensional scaling (MDS) ( 43 , 44 ) was used to demonstrate data homogeneity (Qlucore Omics Explorer 2.2) and identify outliers using cross validation.

Techniques: Gene Expression, Expressing

Journal: BMC Genomics

Article Title: Human growth is associated with distinct patterns of gene expression in evolutionarily conserved networks

doi: 10.1186/1471-2164-14-547

Figure Lengend Snippet: Differential age-associated gene expression. A . Heat map of age-associated changes in gene expression in 87 individuals (0.2 to 29.3 years of age - average 7.7+/−7.0 yrs). 927 gene expression probes were significantly associated with age (ANOVA, false discovery rate (FDR) corrected p-value, q < 0.1, with both gender and study used as co-variates. Supervised hierarchical clustering using Kendell’s dissimilarity and Ward’s method identified three main clusters of gene expression probes: ≤6 years of age [infancy, early childhood group (408 probes)]; >6 to ≤17 years of age [late childhood, puberty group (252 probes)]; and >17 to <30 years of age [adulthood (267 probes)]. Gene expression is shown between +2.5 fold and −2.5 fold, red = increase in gene expression, green = decrease in gene expression. Human growth curve data from normal controls [ , ] shown in relation to the heat map, age groups coloured by upper limit of group bins (years). B. Multi-dimensional scaling (MDS) of the 927 development-related gene expression probes shows distinct development-related clustering; ellipsoids represent 2 standard deviations of normalised gene expression, colour coded by age. Axes represent proportion of variation as defined by MDS (%).

Article Snippet: Model formulation consisted of three stages; first, dimensional scaling using Principal Components Analysis (PCA) and Iso-map multidimensional scaling (MDS) [ , ] was used to demonstrate data homogeneity (Qlucore Omics Explorer 2.2) and identify outliers using cross-validation (Additional file : Figure S1 A&B); secondly, to assess the effects of different distributions of age and gender in each separate data set a sliding window multi-dimensional scaling approach was used.

Techniques: Gene Expression