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Figure 4 | BMC Genomics

Figure 4

From: Transcriptome coexpression map of human embryonic stem cells

Figure 4

Coexpression chromosomal domains of SOX15 (A), PTPRCAP (B), and NGFRAP1 (C), which represent three different coexpression patterns in ES and EB. Left, principal component analysis map. Each dot represents a gene of a domain expressed in ES (blue dots) or EB (brown dots). The wire mesh was constructed based on a standard error of 2. Genes with correlated expression profiles tend to cluster tightly together into a small-size ellipsoid by the wire mesh, while genes with less similar expression profiles form a looser cluster with larger size of ellipsoid. The SOX15 domain is shown to have a higher coexpression level in ES than EB, PTPRCAP domain has a higher coexpression in EB than ES, while NGFRAP1 domain shows a non-differential coexpression pattern between ES and EB. Middle, transcriptome map of the chromosome domain (genomic locations are in mega base pairs). Each gene on the heatmap is indicated. In the SOX15 domain, most genes have higher coexpression index values in ES than in EB. In the PTPRCAP domain, most genes have higher coexpression index values in EB than ES. In the NGFRAP1 domain, most genes have similar coexpression index values between ES and EB. Right , heatmap of gene expression and unsupervised hierarchical cluster analysis. Each column in the heatmap corresponds to an ES or EB sample. Each row represents the relative level of expression of a single gene. The genes are arranged from top to bottom in the same order as they appear on the chromosome from 5' to 3' shown on the transcriptome map. Each gene is denoted by its symbol, followed by the fold-change and ANOVA P value (in brackets) indicating the level of differential expression of the gene between ES and EB. Red, high expression relative to the mean expression; green, low expressions relative to the mean expression; black, no significant change in expression level between the sample and mean.

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