Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

6.3 Copy Number Aberrations Results
hierarchical tag assignment process described above and summarised in fig 6.4.
This showed that most of the transcriptional activity in our cell lines could not
be represented by known transcripts or cDNAs, but perhaps that much of the
regulation might be happening at the non-coding transcriptional level. On av-
erage, in every cell line, less than 45% of tags mapped perfectly to the reference
nuclear genome, i.e. the tags contained within the "Ref_uniq", "Ref_best",
"cDNA_uniq" and "cDNA_best" sets in the non-green portions of fig 6.5.
This indicated that almost half of the transcriptional activity detected in our
cell lines could be traced back to known gene functions, giving us the possi-
bility to correlate gene expression in our cell lines with, for example, known
cancer pathways or other data from similar experiments. Of these 45% tags,
on average 32% were specifically assigned to high-quality reference transcript
models from the widely used Ensembl, RefSeq and Mammalian Gene Collec-
tion (MGC) databases (i.e., belonged to the "Ref_uniq" and "Ref_best" sets).
Reassuringly, other Tag-seq studies have reported similar figures [194,346].
Given that glioblastoma is a heterogeneous tumour, and that our samples were
taken from three distinct glioblastoma patients, we performed an analysis to
observe whether any correlation existed between the cell lines (Fig 6.6) that
would reinforce or weaken that knowledge. We observed the following, calcu-
lating a single expression value for each gene in each cell line by summing the
counts of all tags assigned to that gene: the correlation between the techni-
cal replicates G144 and G144ED was the highest (Pearson R = 0.94), as was
assumable since the two cell lines were derived from the same tumour but in
different laboratories (it should be noted that differences between these repli-
cate measurements can be due to a number of factors in the procedure from
cell line establishment to tag sequencing); the correlation between the two NS
cell lines was also high (R = 0.87); any correlation between GNS cell lines
(G166, G179 and G144) showed larger differences in gene expression profiles
(R ranging from 0.78 to 0.82) than the correlation between the two biological
replicates or the two NS cell lines, as was to be expected since the GNS cell
lines originated from histologically distinct tumours while the NS cell lines
supposedly bore a wild type transcriptional activity.
6.3 Copy Number Aberrations
Since the observed differences in gene expression can be caused by a number
of factors such as chromosomal aberrations (including rearrangements, losses
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