Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-06T13:04:56.537Z
Answers.LastActivityDate: 2017-09-06T13:04:56.537Z
Answers.LastEditDate: 2020-06-18T08:30:41.743Z
Answers.UserDisplayName: Mitra
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-05T13:34:48.177Z
Comments.Text: What effort did you take? Did you look at available data from GEO already?
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-05T14:13:08.310Z
Comments.Text: 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.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-05T14:19:54.207Z
Comments.Text: @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".
Comments.UserDisplayName: 719016
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-05T14:26:14.560Z
Comments.Text: 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).
Comments.UserDisplayName: OrdiNeu
Tags: <rna-seq><ngs><illumina><human>
Title: genes with highest RPKM/FPKM for a human RNA-seq experiment?
ThreadText: # 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**: @username_2 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).  
  
  ---
  
  ## 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.
  
  
  ---
  
  