Answers.Body: <p>The -2 to 2 should be the normalized version of log2 data (maybe mean or median normalization). This is commonly used in heatmaps to show downregulated value vs. upregulated value.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-03T04:23:16.163Z
Answers.LastActivityDate: 2023-02-03T04:23:16.163Z
Answers.UserDisplayName: Pete Kittinun
Body: <p>This is a follow up to my question posted here
  <a href="https://bioinformatics.stackexchange.com/questions/18850/processing-proteomics-data">Processing proteomics data</a></p>
  <p>In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article &quot;Diabetes causes marked inhibition of mitochondrial metabolism in pancreatic β-cells&quot; (figures from here: <a href="https://pubmed.ncbi.nlm.nih.gov/31171772/" rel="nofollow noreferrer">link</a>).</p>
  <p>I would like to know how to generate the following heat map from the normalized abundances reported.</p>
  <p>Fold change heatmap:
  <a href="https://i.sstatic.net/ETP3m.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ETP3m.png" alt="enter image description here" /></a></p>
  <p>Abundance:
  <a href="https://i.sstatic.net/bgGte.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/bgGte.png" alt="enter image description here" /></a></p>
  <p>Figure description:</p>
  <blockquote>
  <p>Heat maps of relative mRNA and protein levels of the indicated genes
  in islets isolated from control and 2-week diabetic βV59M mice. Each
  box corresponds to a different animal. Colour indicates log2
  fold-change. Heat map: TCA cycle. Red, proteins upregulated in
  diabetes; blue, proteins downregulated in diabetes. Grey, no change or
  not detected. PDK1, pyruvate dehydrogenase kinase 1. Abundance:
  Abundance of the indicated proteins, quantified by mass spectrometry,
  in islets isolated from control (black, Ctrl, n = 4) and 2-week
  diabetic βV59M (white, Diab, n = 4) mice.</p>
  </blockquote>
  <p>I am not able to understand how the log2 fold-change is computed from the abundance.
  For instance, if we consider <code>PDK1</code> (first panel) the abundance measure of control is ~50000 and diabetic is ~200000. Heat map says log2 fold-change (in the figure description added above). What is the fold-change that is referred to? From what is shown, I think this is not diabetic/control fold change; we see two panels (i.e one for control (4 samples) and the other for diabetic (4 samples)) and not a single panel. Since the legend is from (-2 to 2) I think these values are not log2 (abundance) as well.</p>
  <p>Could someone please clarify how the heat map has been generated from the abundance measures? Basically, I want to know how to generate the first heatmap figure from abundance plots.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-18T14:21:33.613Z
Comments.Text: I'll delete this comment later - mods complaint - what I'll do put up a python seaborn solution to your data under `pandas`, but I'm not around until much later in the week. Its  fairly easy to do, so you don't have to hang around.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-19T04:44:27.993Z
Comments.Text: Hi @M__  Thanks for the comment. I managed to plot the heatmap in python. But I am having some confusion regarding the figure description and the heatmap shown in the article. I'll share a detailed edit today.
Comments.UserDisplayName: Natasha
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-14T15:32:18.727Z
Comments.Text: Briefly ... that is absolutely correct - its not clear. The 2 to -2 is log10 (standard log) there is no other explanation. The appendix of the paper used log2 because it stated this (it is weird because natural log is would be the obvious choice in that scenario). This heatmap must be standard log. The authors MUST state the transformation and they do not appear to have done this. I will forward heatmap stuff - as comments.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-14T15:34:05.617Z
Comments.Text: I do have sympathy with the OPs project - this is an unnecessarily difficult project, which is outside their control.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-14T15:35:43.827Z
Comments.Text: I got a reply yesterday from the corresponding author on the diabetic vs. control labels of the samples.
Comments.UserDisplayName: Natasha
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-14T15:37:06.933Z
Comments.Text: Thats good, happy the project is moving forward
Comments.UserDisplayName: M__
Tags: <proteins><proteomics><heatmap><mass-spectrometry><meta-analysis>
Title: Heat map of protein expression from normalized abundance
ThreadText: # Heat map of protein expression from normalized abundance
  
  (Asked by: username_0 on 2022-04-14)
  
  This is a follow up to my question posted here
  [Processing proteomics data](https://bioinformatics.stackexchange.com/questions/18850/processing-proteomics-data)
  
  In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes marked inhibition of mitochondrial metabolism in pancreatic β-cells" (figures from here: [link](https://pubmed.ncbi.nlm.nih.gov/31171772/)).
  
  I would like to know how to generate the following heat map from the normalized abundances reported.
  
  Fold change heatmap:
  [![enter image description here](https://i.sstatic.net/ETP3m.png)](https://i.sstatic.net/ETP3m.png)
  
  Abundance:
  [![enter image description here](https://i.sstatic.net/bgGte.png)](https://i.sstatic.net/bgGte.png)
  
  Figure description:
  
  > Heat maps of relative mRNA and protein levels of the indicated genes
  > in islets isolated from control and 2-week diabetic βV59M mice. Each
  > box corresponds to a different animal. Colour indicates log2
  > fold-change. Heat map: TCA cycle. Red, proteins upregulated in
  > diabetes; blue, proteins downregulated in diabetes. Grey, no change or
  > not detected. PDK1, pyruvate dehydrogenase kinase 1. Abundance:
  > Abundance of the indicated proteins, quantified by mass spectrometry,
  > in islets isolated from control (black, Ctrl, n = 4) and 2-week
  > diabetic βV59M (white, Diab, n = 4) mice.
  
  I am not able to understand how the log2 fold-change is computed from the abundance.
  For instance, if we consider `PDK1` (first panel) the abundance measure of control is ~50000 and diabetic is ~200000. Heat map says log2 fold-change (in the figure description added above). What is the fold-change that is referred to? From what is shown, I think this is not diabetic/control fold change; we see two panels (i.e one for control (4 samples) and the other for diabetic (4 samples)) and not a single panel. Since the legend is from (-2 to 2) I think these values are not log2 (abundance) as well.
  
  Could someone please clarify how the heat map has been generated from the abundance measures? Basically, I want to know how to generate the first heatmap figure from abundance plots.
  
  **Tags:** proteins, proteomics, heatmap, mass-spectrometry, meta-analysis
  
  > **Comments:**
  > **username_1**: Briefly ... that is absolutely correct - its not clear. The 2 to -2 is log10 (standard log) there is no other explanation. The appendix of the paper used log2 because it stated this (it is weird because natural log is would be the obvious choice in that scenario). This heatmap must be standard log. The authors MUST state the transformation and they do not appear to have done this. I will forward heatmap stuff - as comments.  
  > **username_1**: I do have sympathy with the OPs project - this is an unnecessarily difficult project, which is outside their control.  
  > **username_0**: I got a reply yesterday from the corresponding author on the diabetic vs. control labels of the samples.  
  > **username_1**: Thats good, happy the project is moving forward  
  > **username_1**: I'll delete this comment later - mods complaint - what I'll do put up a python seaborn solution to your data under `pandas`, but I'm not around until much later in the week. Its  fairly easy to do, so you don't have to hang around.  
  > **username_0**: Hi @username_1  Thanks for the comment. I managed to plot the heatmap in python. But I am having some confusion regarding the figure description and the heatmap shown in the article. I'll share a detailed edit today.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-02-03. Score: 1
  
  The -2 to 2 should be the normalized version of log2 data (maybe mean or median normalization). This is commonly used in heatmaps to show downregulated value vs. upregulated value.
  
  
  ---
  
  