In Figure S8ainAdditional File 4, we show the mean pathway aberration profiles for five pathways that are differentially aberrant in the three KIRC subgroups.
Using mummichog [ 32], we found that metabolites that changed significantly in response to developmental temperature were enriched for six metabolic pathways in male flies, and for seven pathways in female flies (Tables 1 and 2).
In Figure 4a, we show the mean pathway aberration profiles for nine pathways that are differentially aberrant in the 12 GBM subgroups.
We acknowledge that SignaLink 2 contains data for seven pathways, while some resources (e.g., KEGG, Reactome) contain significantly more pathways.
We identified most of the genes for two pathways that catalyze two modifications on the wobble anti-codon uridine tRNA U34.
To verify the usefulness of the processed expression data for extracting transcriptional regulators, we initially interrogated the datasets for two pathways whose regulation is already well understood.
Among all subjects, enrichment for six pathways was observed (Fisher's exact p < 0.05) including the antigen presentation pathway, propanoate metabolism, interferon signaling, primary immunodeficiency signaling, the coagulation system, and the pantothenate and CoA biosynthesis pathway (see Figure 2A).
Almost all pathways in the top 20 list are supported by literature evidence: only for five pathways in the FTC list we were not able to find support in the literature.
At a molecular level there is evidence for two pathways indicating that vinculin may act as a tumour suppressor by inhibiting ERK (Extracellular signal-Regulated Kinase), a protein which has a key role in the regulation of cell proliferation.
In parallel, the Kap network could allow proteins to acquire mutations in a region that disrupts a localization signal for one pathway without compromising their proper localization.
