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.

  • 2
    $\begingroup$ What effort did you take? Did you look at available data from GEO already? $\endgroup$
    – benn
    Commented Sep 5, 2017 at 13:34
  • $\begingroup$ 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 Ryan
    Commented Sep 5, 2017 at 14:13
  • $\begingroup$ @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". $\endgroup$
    – 719016
    Commented Sep 5, 2017 at 14:19
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    $\begingroup$ 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). $\endgroup$
    – OrdiNeu
    Commented Sep 5, 2017 at 14:26

1 Answer 1


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.


  • 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.


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