Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Biological implications of RPKM value

    Hello everyone,

    Currently, I am going deep-through our expression database (bacterial RNA-seq data) in order to get the maximum information possible. I stumbled across very simple but still very important question: From what point can we say that a gene is fairly-well expressed in terms of RPKM value? For example, if I have a RPKM value of 50, with what confidence can I say that that gene is indeed expressed, hence important for the cell in given conditions?

    Would it be safe to compare to the mean expression of all genes, or perhaps compare to the expression of some HKG or even tRNA or rRNA?

    Thank you in advance for your opinion,

    TP

  • #2
    if I have a RPKM value of 50, with what confidence can I say that that gene is indeed expressed, hence important for the cell in given conditions?
    Depends on the experiment. My lab throws in ERCC spike-ins into the preps, and if the spike-ins still show appropriately linear behavior at 1 RPKM, then we figure other genes at 1 RPKM are also okay, quantitatively.

    In my lab, we usually say that 0.5 RPKM or 1 RPKM are good cutoffs.

    An RPKM of 50 means that if you had 1 million reads in your experiment, and you are looking at a 1 kb transcript, you have 50 reads aligning to that transcript. If you have 5 million reads, that's 250 reads on that transcript. That's a pretty solid number, unless your prep has lots of PCR artifacts.

    Comment


    • #3
      Thank you for your input on this.

      I plotted a histogram of RPKM value and this is what I got:


      The median is about 36, but goes from 0 to 140K. So, I guess RPKM of 50 is pretty solid as you suggested, but what I do with low RPKM values? 1 or 2...? Where can I put a cutoff? Is it safe to say that under 10, it is a weak expression, 10-100 is "normal" expression and over 100 is high expression?

      Thanks again,
      TP

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Exploring the Dynamics of the Tumor Microenvironment
        by seqadmin




        The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
        07-08-2024, 03:19 PM
      • seqadmin
        Exploring Human Diversity Through Large-Scale Omics
        by seqadmin


        In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
        06-25-2024, 06:43 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 07-19-2024, 07:20 AM
      0 responses
      38 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-16-2024, 05:49 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-15-2024, 06:53 AM
      0 responses
      60 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-10-2024, 07:30 AM
      0 responses
      43 views
      0 likes
      Last Post seqadmin  
      Working...
      X