A thumbnail overview of the result of the two-way average-linkage hierarchical clustering of 38 arrays (columns) and 1532 isoforms (rows), as described in ref 30

<p><b>Copyright information:</b></p><p>Taken from "Profiling alternatively spliced mRNA isoforms for prostate cancer classification"</p><p>BMC Bioinformatics 2006;7():202-202.</p><p>Published online 11 Apr 2006</p><p>PMCID:PMC1458362.</p><p>Copyright © 2006 Zhang et al; licensee BioMed Central Ltd.</p> (Zoom-in view of the array clustering dendrogram. The two array clusters, C1 and C2, are enriched by normal samples and tumor samples, respectively. Cluster C2 is formed by two sub-clusters, reflecting differences in tumor percentage and stroma. (Isoform signatures up- or down-regulated in different array clusters. (The result of SVD. () The percentage of variation (y-axis) captured by each principal component (x-axis). (The low dimensional projection of arrays in the 3D space spanned by the first three principal components. SVD identified the same hierarchical structure as revealed by hierarchical clustering

Dysregulated gene expression in top three Map Folders in adult autistic prefrontal cortex and differentially affected M-Pathways of young and adult autistic cases.

<p>(A) Graph on the right shows fold change of genes in cell differentiation, mitogenic signaling, and apoptosis and survival Map Folders. Colors on fold change graph correspond to circles on the left depicting network maps in each category. From each category of differentially expressed genes in adult autistic vs. adult control posthoc comparison (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002592#pgen.1002592.s008" target="_blank">Table S4</a>), gene networks on the left were created using MetaCore Network Analysis. (B) Top differentially affected M-pathway comparisons of dysregulated genes between adult and young autistic cases. Bars represent significance of listed pathways. Orange = adult; blue = young; faded color = FDR>0.1 or p>0.05.</p

Dysregulated gene expression in top two MetaCore Map Folders in autism independent of age.

<p>Graph on left shows fold change of genes in DNA damage response and apoptosis and survival Map Folders. The third most significant map folder is depicted in Figure S3. Colors on fold change graph correspond to circles on the left depicting network maps in each category. From each category of differentially expressed genes in the all autistic vs. all control comparison (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002592#pgen.1002592.s009" target="_blank">Table S5</a>), networks were created using MetaCore Network Analysis.</p

Dysregulated gene expression in developmental M-Pathways and Process Networks in young autistic prefrontal cortex.

<p>From differentially expressed genes of young autistic vs. young control cases (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002592#pgen.1002592.s006" target="_blank">Table S2</a>), networks were created using MetaCore Network Analysis. Colors on fold change graph correspond to circles on the right depicting network maps in each category. Yellow = differentially expressed genes in two or more functional domains. Overlapping circles = differentially expressed genes common to two domains.</p

MetaCore process networks and network maps in autism based on gene deletions located in CNVs from DLPFC, and genetic association results.

<p>Autistic cases had significant enrichment of MetaCore process networks in genes contained within total CNVs (A) and filtered CNVs (i.e., not present in the Database of Genomic Variants) using PennCNV (B) and CNVision (C). Blue bars = controls; red bars = autistic cases. (D) MetaCore network analysis of the top three enriched MetaCore process networks in (B). Symbols in (D) represent gene types or associations. Genes with blue circles were identified autistic CNVs; genes without circles were summoned by the database to complete network. Pink lines = canonical pathway connections. (E) Gene sets tested in set-based association analysis using PLINK in Broad/JHMI and CHOP datasets, number of genes in each set, database from which genes were taken and p-values of associations.</p

MetaCore Pathway Map Folders (left) and M-Pathways (right) in three ANOVA-based analyses.

<p>(A–C) MetaCore Map Folders and M-Pathways identified in posthoc young autism vs. young control analysis (p<0.05, FDR = 0.1; A), posthoc adult autism vs. adult control analysis (p<0.05, FDR = 0.1; B) and diagnosis main effect analyses comparing all autism and all control cases (Top 25; C). P-values and numbers of network objects/ratios of differentially expressed genes are shown.</p