<p>As asked as it is, the answer is probably no.</p>
<p>Indeed, the highest expressed RPKM/FPKMs will be different from one condition (or tissue) to another one for example.</p>
<p>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.</p>
<p>Now, if you want to compare your results to an outside source, I recommend checking the <a href="https://www.ebi.ac.uk/gxa/home" rel="noreferrer">EBI gene expression Atlas</a>* and more specifically the Baseline expression experiments.</p>
<p>Pro-tips:</p>
<ul>
<li>You can filter the genes based on their nature (eg, mRNA) and/or their expression.</li>
<li>You can also visualise the overall expression of a specific gene across several experiments.</li>
</ul>
<p>*Disclaimer: I am related to this project myself.</p>

CC BY-SA 3.0
2017-09-06T13:04:56.537Z
2017-09-06T13:04:56.537Z
2020-06-18T08:30:41.743Z
Mitra
<p>Which genes/transcripts show up as having the highest RPKM/FPKM on a human RNA-seq experiment? Is it usually the same genes/transcripts?</p>

<p>EDIT: mRNAs (e.g. poly-A RNA-seq preps) and not including small RNAs.</p>

CC BY-SA 3.0
2017-09-05T13:34:48.177Z
What effort did you take? Did you look at available data from GEO already?
benn
CC BY-SA 3.0
2017-09-05T14:13:08.310Z
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.
Devon Ryan
CC BY-SA 3.0
2017-09-05T14:19:54.207Z
@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".
719016
CC BY-SA 3.0
2017-09-05T14:26:14.560Z
In that case, you may be looking for [housekeeping genes](https://en.wikipedia.org/wiki/Housekeeping_gene) -- this doesn't quite answer the question as stated (they aren't always the highest expressed, but they are usually present).
OrdiNeu
<rna-seq><ngs><illumina><human>
genes with highest RPKM/FPKM for a human RNA-seq experiment?
# genes with highest RPKM/FPKM for a human RNA-seq experiment?

(Asked by: username_0 on 2017-09-05)

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.

**Tags:** rna-seq, ngs, illumina, human
> **Comments:**
> **username_1**: What effort did you take? Did you look at available data from GEO already?  
> **username_2**: 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.  
> **username_0**: @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".  
> **username_3**: In that case, you may be looking for [housekeeping genes](https://en.wikipedia.org/wiki/Housekeeping_gene) -- this doesn't quite answer the question as stated (they aren't always the highest expressed, but they are usually present).  

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## 1 answers

### Answer by username_4 on 2017-09-06. Score: 6 | Accepted answer

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](https://www.ebi.ac.uk/gxa/home)\* 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.


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