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Old 01-17-2014, 12:52 AM   #3
still a novice
Location: Cardiff

Join Date: Jul 2010
Posts: 34

Thanks Bukowski for your reply. The aim for this experiment is to see if there are specific genes/biological pathways that are massively up regulated in these tumours, some mouse work has identified increased expression of some members of the wnt pathway so we'd like to be able to replicate those findings in the human and also look for more (the mouse work was microarray). There is also the aim to look for potential gene fusions, alt splicing and RNA editing. We know the tumour is unlike any normal tissue and we are expecting the main driver genes/pathways to be massively over expressed and therefore we are not looking at subtle changes and so that is why we are hoping we may be able to get some kind of reference brain transcriptome data to use as a control.
I'm also wondering if we could normalise our data using some housekeeping genes and compare to reference brain datasets? Apparently the pituitary is a bag of growth hormone so I'm not sure if normal pituitary is a good or bad thing to compare against, my gut instinct is that it is a good comparison but I wonder if there is a whole brain transcriptome dataset out there somewhere?
This is also very much a learning process for our group and so we want to play around with some RNAseq data and optimise an analysis pipeline, I should also add we're doing exome on blood and tumour to look for driver somatic mutations in these samples as well.
I hope that gives you a better understanding of the project and any feedback would be much appreciated

Cheers H
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