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. 2018 Oct 24;47(Database issue):D736–D744. doi: 10.1093/nar/gky997

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© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Study-centered data exploration. (A) PCA of normal hindbrain, Shh-medulloblastoma and Wnt-medulloblastoma ECs (study E-GEOD-73753). (B) Gene set enrichment analysis of normal hindbrain ECs versus Shh-medulloblastoma ECs. The upregulated gene sets are shown in red, the downregulated gene sets are shown in blue. (C) Differential analysis of normal hindbrain ECs versus Shh-medulloblastoma ECs shown in volcano plot; some highly deregulated proliferation-associated genes are indicated. (D) Gene expression heatmap of normal hindbrain ECs versus Shh-medulloblastoma and Wnt-medulloblastoma. The high-gene expression levels are shown in red, the low-expression levels in blue. (E) Expression of the indicated genes in normal hindbrain ECs and Shh-medulloblastoma ECs. (F) Metabolic gene set enrichment analysis of normal hindbrain ECs versus Shh-medulloblastoma ECs. The upregulated gene sets are shown in red, the downregulated gene sets are shown in blue. (G and H) Differential analysis of normal hindbrain ECs versus Shh-medulloblastoma ECs for the subset of metabolic genes (G) and transcription factors (H) shown as a volcano plot. Abbreviations—Ccna2: cyclin A2; Mki67: marker of proliferation ki67; NES: normalized enrichment score; Rrm2: ribonucleotide reductase regulatory subunit M2; Shh: Sonic Hedgehog; TEC: tumor endothelial cell; Top2a: topoisomerase 2 alpha; Uck2: uridine-cytidine kinase 2.