Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

6.7 Isoform Differential Expression Results
may have therapeutic relevance, as inhibitors of their homolog PARP1 are in
clinical trials for brain tumours [270]. Our comparison between GNS and NS
cell lines, thus, highlights genes and pathways that are known to be affected in
glioma as well as novel candidates, suggesting that the GNS vs NS comparison
is a promising approach for further understanding molecular aspects of glioma.
6.7 Isoform Differential Expression
To establish Tag-seq as a sensitive technique for the identification of tran-
script isoforms differentially expressed between our GNS and NS libraries, we
performed a parametric and a non-parametric test on the genes identified by
multiple tag mappings using the "Ref_best" collection (see Fig 6.5).
With the non-parametric χ 2 test, 2,682 isoforms were found to be differentially
expressed as detected by the sum over all tags for each isoform. With the para-
metric approach, in which the logarithmic ratio of expression method adapted
from Morrissy et al [346] was used, we computed a ratio change for each pair
of tags that identified an isoform, so that a total of 2,040 differentially ex-
pressed isoforms were detected. The two methods share a total of 1,454 genes
that have differentially expressed isoforms in the GNS cell lines with respect
to the NS cell lines at significant levels (p-value2 for parametric), with 1,228 genes uniquely identified by the logarithmic
method and 586 genes uniquely identified by the non-parametric method.
In the attempt to focus on isoforms relevant to the pathways affected in
glioma, we overlaid both lists of differentially expressed isoforms on the in-
tegrated glioblastoma pathway described in section 7.5 and shown in figure
7.8. This highlighted the presence of 48 matching genes from the logarithmic
(non-parametric) method and 57 matching genes from the parametric χ 2 test
method, with 35 genes shared between the two methods. Each of the 35 genes,
as well as the 13 genes identified exclusively through the logarithmic method
and the 22 genes identified exclusively through the parametric χ 2 test method,
were manually scrutinised on the University of California Santa Cruz (UCSC)
genome browser by adding our tag mappings as a custom track together with
the UCSC gene track and the gene predicted Ensembl track, both in "full"
mode for the NCBI37.2/Ensembl 64 human genome assembly. For the follow-
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