Body: <p>Our study shows that gene A knockout will down-regulate cell cycle-related genes in some cell lines. My aim is to understand whether cell cycle-related genes are down regulated on the transcriptional or translational level upon gene A knockout.</p>
  <p>I plan to compare the transcript and protein abundance of cell cycle-related genes between two groups of cell lines (1st group: sensitive to gene A knockout; 2nd group: not sensitive to the knockout). May I ask how can I do this? Are there any tools, databases and papers related to my goal? Thank you very much!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-23T15:05:18.633Z
Comments.Text: This sounds more like a wet-lab question than a bioinformatics one. You are basically asking about how to run quantitative PCR or simlar techniques to measure transcript abundance and whatever would be used (sorry, no idea) to measure protein abundance, right? Once you have your data, we can help process them, but we can't help on the experimental side.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-25T22:35:41.657Z
Comments.Text: There are a large number of issues with this question. The first issue with the question is we don't know what organism is being studied, I might guess at yeast (traditional cycle model) - but that would be weird because there's loads of studies like that on yeast. It is very unlikely to be yeast because the RNA vs protein will be understood in detail. The second is what knock-down is it? ... and so on. Then there is the unfocused issue of the question about a comparison between transcriptomics vs. proteomics and how to analyse the relationship between them.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-25T22:37:56.420Z
Comments.Text: To simply answer the question, papers - yeast. Method of comparison supervised machine learning.
Comments.UserDisplayName: M__
Tags: <correlation><data-mining><transcriptome-regulation>
Title: How to investigate the correlation between transcript and protein abundance?
ThreadText: # How to investigate the correlation between transcript and protein abundance?
  
  (Asked by: username_0 on 2023-02-23)
  
  Our study shows that gene A knockout will down-regulate cell cycle-related genes in some cell lines. My aim is to understand whether cell cycle-related genes are down regulated on the transcriptional or translational level upon gene A knockout.
  
  I plan to compare the transcript and protein abundance of cell cycle-related genes between two groups of cell lines (1st group: sensitive to gene A knockout; 2nd group: not sensitive to the knockout). May I ask how can I do this? Are there any tools, databases and papers related to my goal? Thank you very much!
  
  **Tags:** correlation, data-mining, transcriptome-regulation
  
  > **Comments:**
  > **username_1**: This sounds more like a wet-lab question than a bioinformatics one. You are basically asking about how to run quantitative PCR or simlar techniques to measure transcript abundance and whatever would be used (sorry, no idea) to measure protein abundance, right? Once you have your data, we can help process them, but we can't help on the experimental side.  
  > **username_2**: There are a large number of issues with this question. The first issue with the question is we don't know what organism is being studied, I might guess at yeast (traditional cycle model) - but that would be weird because there's loads of studies like that on yeast. It is very unlikely to be yeast because the RNA vs protein will be understood in detail. The second is what knock-down is it? ... and so on. Then there is the unfocused issue of the question about a comparison between transcriptomics vs. proteomics and how to analyse the relationship between them.  
  > **username_2**: To simply answer the question, papers - yeast. Method of comparison supervised machine learning.  
  
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  ## 0 answers
  
  