GSE51412
Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation
Genome-wide transcriptome analyses have allowed for systems-  level insights into gene regulatory networks. Due to the limited depth of   quantitative proteomics, however, our understanding of post-transcriptional   gene regulation and its effects on protein complex stoichiometry are lagging   behind.   Here, we employ deep sequencing and iTRAQ technology to determine transcript   and protein expression changes of a Drosophila brain tumour model at near   genome-wide resolution. In total, we quantify more than 6,200 tissue-specific   proteins, corresponding to about 70% of all transcribed protein-coding genes.   Using our integrated data set, we demonstrate that post-transcriptional gene   regulation varies considerably with biological function and is surprisingly   high for genes regulating transcription. We combine our quantitative data with   protein-protein interaction data and show that post-transcriptional mechanisms   significantly enhance co-regulation of protein complex subunits beyond   transcriptional co-regulation. Interestingly, our results suggest that only   about 11% of the annotated Drosophila protein complexes are co-regulated in   the brain. Finally, we refine the composition of some of these core protein   complexes by analysing the co-regulation of potential subunits.  Our comprehensive transcriptome and proteome data provide a rich resource for   quantitative biology and offer novel insights into understanding post-  transcriptional gene regulation in a tumour model. Overall design: Transcriptomes of 1-3 day old adult female Drosophila melanogaster heads of control and brat mutant were generated by deep sequencing, in triplicate, using Illumina GAIIx.