Which genes/transcripts show up as having the highest RPKM/FPKM on a human RNA-seq experiment? Is it usually the same genes/transcripts?
EDIT: mRNAs (e.g. poly-A RNA-seq preps) and not including small RNAs.
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2$\begingroup$ What effort did you take? Did you look at available data from GEO already? $\endgroup$– bennCommented Sep 5, 2017 at 13:34
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$\begingroup$ I'm guessing there's some missing context here of the form, "We've done a bunch of RNAseq experiments and X, Y, Z always show up as having the highest FPKMs. Have other people seen this or are we just doing something wrong?" If so, please include it. $\endgroup$– Devon RyanCommented Sep 5, 2017 at 14:13
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$\begingroup$ @DevonRyan the context is more: "here is a handful of genes that always come up on top for a human sample. If you don't see them, something may have happened". $\endgroup$– 719016Commented Sep 5, 2017 at 14:19
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1$\begingroup$ In that case, you may be looking for housekeeping genes -- this doesn't quite answer the question as stated (they aren't always the highest expressed, but they are usually present). $\endgroup$– OrdiNeuCommented Sep 5, 2017 at 14:26
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As asked as it is, the answer is probably no.
Indeed, the highest expressed RPKM/FPKMs will be different from one condition (or tissue) to another one for example.
Then, you may also have technical artefacts due to the wet-lab part or to the normalisation. For example, mitochondrial genes are often reported in the top expressed genes.
Now, if you want to compare your results to an outside source, I recommend checking the EBI gene expression Atlas* and more specifically the Baseline expression experiments.
Pro-tips:
- You can filter the genes based on their nature (eg, mRNA) and/or their expression.
- You can also visualise the overall expression of a specific gene across several experiments.
*Disclaimer: I am related to this project myself.
