Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

7.5 Glioblastoma Pathway Analysis Results
Naturally, we wanted to make use of the resource ourselves and used it to
visualise gene expression changes in the context of the molecular networks
represented. The complete pathway has a total of 245 nodes, of which 57 are
not genes and the remaining 188 are single genes. The nodes representing
genes can be recognised by their distinct circular shapes that are unique to
this category. Of the 57 non gene nodes: 22 are families of proteins, rep-
resented by a diamond shape; eight are complexes of proteins, represented
by a hexagon shape; six are non-proteic molecules, represented by a vee-like
shape; the remaining 20 define end-processes such as "apoptosis", "cell signal-
ing" and "protein synthesis" and are represented by round rectangular shapes.
The only isoforms represented in the pathway are the two isoforms of gene
CDKN2A labeled as CDKN2A and CDKN2A:ARF (Table 7.7). The dataset
Table 7.7: Node assignment in the glioblastoma pathway. The colour of the nodes
representing genes and isoforms is only grey at the default pathway level. When
expression data are overlaid on the network the gene nodes will become coloured
according to a customisable colour palette.
Node type Number of nodes Node shape Node colour
Gene families 22 Diamond Beige
Cellular Processes 20 Round Rectangle Beige
Non-proteic molecules 6 Vee Beige
Complexes 8 Hexagon Beige
Genes 186 Circle Grey, default
Isoforms 2 Circle Grey, default
Total 245
of differentially expressed genes from the Tag-seq expression dataset contains
739 genes at an FDR of 10%. By overlaying the expression data for the 739
differentially expressed genes over the 188 gene nodes in the pathway, we found
that 70 genes were differentially expressed between GNS and NS cell lines at
10% FDR. Of these 70 genes, 51 were up-regulated in GNS cell lines (red colour
gradient), and 19 were down-regulated in GNS cell lines (blue colour gradient)
(Fig 7.8). The intensity of the colour reflects the value of the log2(FC) be-
tween GNS and NS cell lines and the values defining the red and blue colour
gradients were specifically taken from the same colour gradients defined in
the qRT-PCR heatmap of figure 6.13 and the tumour expression correlation
heatmap of figure 7.4.
190