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Old 10-20-2011, 03:20 AM   #1
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Location: Berlin, Germany

Join Date: May 2011
Posts: 3
Question Constructing library of tissue-specific genes

Hi all,

first of all, I have to say this site is amazing with all its discussions going on. I found new impulses and great hints here for writing up my diploma thesis!

My question:
I am trying to build a library of differentially genes for further analysis, e.g. I don't need information on which genes are specific for which tissue.

My data is Illumina HiSeq2000 with 16 tissues(adipose, adrenal,...) and two technical replicates(75bp SingleEnd, 50bp PairedEnd). I already mapped the data with tophat and counted reads for annotated refSeq genes and normalized for transcript-length.

My idea is genes which show high variance across all 16 samples in both experiments are likely to be tissue-specific. Genes with low variance are simply broadly expressed through the samples and don't contribute much to the overall variance of the experiment.

Do you think it's a good approach to simply identify genes which describe a huge amount of the overall variance best for each experiment(75bp, 50bp_PE) and then look at the intersect to rule out some false positives.
But I don't have any p_val verification how likely an assignment is.

Thanks for your thoughts,
johannes.helmuth is offline   Reply With Quote