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Comparing benign osteoblastomas with osteosarcomas identified cell cycle regulation as the most prominently changed pathway.
We did not find any changed pathway shared by genetically normal (clone 8 without CNV) and abnormal clones (clone 2 and 6, both with CNV).
Gene set enrichment analysis (GSEA) was used to examine the changed pathway expression; the gsealmPerm function from the GSEAlm library was modified to test for bidirectional enrichment in KEGG pathways.
Their analysis identified the Thrombin signaling and protease-activated receptors pathway, which is known to be involved in the angiogenesis of lung cancer, as the most frequently changed pathway.
These comparisons can reveal changes in developmental logic between taxa by identifying gene losses during evolution that must result in changed pathway functioning, and similarly identify genes recruited to developmental regulatory roles in particular lineages.
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The statistical analysis resulted in seven significantly changed pathways (Z-score > 1.96, p-value < 0.05, minimum of three changed genes) (see Table 1).
The outcome of the pathway statistics in PathVisio is a list of significantly changed pathways.
First, all significantly changed pathways were combined and visualized with Cytoscape 3.1.1.
We performed Path-net analysis to generate an interaction network that included these significantly changed pathways.
The significantly changed pathways of amino acid biosynthesis are visualized by MetNet Plug-ins for Cytoscape http://www.metnetdb.org/MetNet_fcmodeler.htm.htm
The significantly changed pathways included galactose and sucrose degradation (P value = 0.017, 0.028 respectively) at 20 DAA.
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