text: user3186: This is a follow up to my question posted here
  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).
  I would like to know how to generate the following heat map from the normalized abundances reported.
  Fold change heatmap:
  
  Abundance:
  
  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.
  
  user16898: 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.
  
original_text: 3186: <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.stack.imgur.com/ETP3m.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/ETP3m.png" alt="enter image description here" /></a></p>
  <p>Abundance:
  <a href="https://i.stack.imgur.com/bgGte.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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>
   16898: <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>
  