Answers.Body: <p>In scRNA-seq clusters are groups of cells with similar transcriptomes typically defined by graph based methods (e.g. leiden, louvain) or more rarely k-means.</p>
  <p>Marker genes could be genes that are known to be highly expressed (or better specifically expressed) in a particular cell type (e.g. CD3E is a T cell marker). You can visualize the expression of such marker genes on a UMAP/t-SNE without doing any clustering.</p>
  <p>When talking about positive and negative markers, I assume the reference is too differentially expressed genes between different clusters. Typically simple differential expression tests are conducted (e.g. Wilcoxon rank sum) between each individual cluster and the other collective clusters. The upregulated differentially expressed genes could be considered positive markers and downregulated genes negative markers.</p>
  
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Answers.Text: What do you mean upregulated and and downregulated? I do not understand about them? Also, the 200 genes I mentioned, basically we cannot say those genes are marker genes for cluster A?
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Answers.Body: <p>May I reignite this conversation? I don't really want to start a new topic for this because it's closely related to the op's question and the answers.</p>
  <p>What if you do the wilcoxon/MAST etc statistical tests for the clusters and look for a marker in a speicifc cluster. Let's say CD4 in cluster X. Cluster X doesn't have CD4 as statistically significant (so p_adj &gt; 0.05), OR you biologically you would exprect cluster X as a CD4 positive population but that statistical test lists CD4 as a statistically significant negative marker BUT with -0.1 log2FC.</p>
  <p>Where would you categorize cluster X in these 2 cases? (1.)not coming up as a significant DEG 2.) significant but with minimal negative log2FC although you expect it as positive side note: percent of cells expressing the given marker is very close in clusterX vs everything else.)</p>
  <p>Thanks in advance.</p>
  
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Answers.Text: Is this an actual answer or a follow up question/request for clarification of the original question?
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Answers.Text: I intended this as a follow up question. OP asked basically what is a positive and a negative marker. Answers stated that we can look at positive LFC significant DEGs as positive, and negative LFC significant DEGs (from differential gene expression analysis, like FindAllMarkers used in seurat package). And i brought up the scenario i am interested to know the answer for. Maybe it can be it's own thread but i thought i try this way, idk.
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Answers.Body: <p>A positive marker is a gene that is overexpressed in a cell population compared to other populations.</p>
  <p>A negative marker is a gene that is underexpressed in a cell population compared to other populations.</p>
  <p>I think the Seurat FindMarkers function has an option to output Log2FoldChange as well as the marker names. In this case the positive markers will have a positive Log2FoldChange, and the negative markers will have a negative Log2FoldChange.</p>
  <p>Both positive and negative markers can be used to describe a cell population. In the research that I've done in the past, there's a particular type of dendritic cell that is only distinguished from another dendritic cell type based on cell surface markers that it <em>doesn't</em> have; our own name for these DCs was &quot;Triple negative&quot;.</p>
  
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Body: <p>I am learning about the marker genes and clustering by Seurat in scRNA-seq datasets. However, I am confused about the term positive marker and negative marker. What I understand is the marker genes of a cluster is the genes which are highly expressed (high counts) in the cells of that cluster. Let's say cluster A has 200 genes. My questions are:</p>
  <p>Can I say that those 200 genes are marker genes for cluster A?
  How to determine which marker genes are positive marker genes and which are negative marker genes?</p>
  
Tags: <scrnaseq><gene><seurat><clustering>
Title: Positive marker and negative marker in scRNA-seq datasets
ThreadText: # Positive marker and negative marker in scRNA-seq datasets
  
  (Asked by: username_0 on 2021-06-09)
  
  I am learning about the marker genes and clustering by Seurat in scRNA-seq datasets. However, I am confused about the term positive marker and negative marker. What I understand is the marker genes of a cluster is the genes which are highly expressed (high counts) in the cells of that cluster. Let's say cluster A has 200 genes. My questions are:
  
  Can I say that those 200 genes are marker genes for cluster A?
  How to determine which marker genes are positive marker genes and which are negative marker genes?
  
  **Tags:** scrnaseq, gene, seurat, clustering
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_1 on 2021-06-09. Score: 1
  
  In scRNA-seq clusters are groups of cells with similar transcriptomes typically defined by graph based methods (e.g. leiden, louvain) or more rarely k-means.
  
  Marker genes could be genes that are known to be highly expressed (or better specifically expressed) in a particular cell type (e.g. CD3E is a T cell marker). You can visualize the expression of such marker genes on a UMAP/t-SNE without doing any clustering.
  
  When talking about positive and negative markers, I assume the reference is too differentially expressed genes between different clusters. Typically simple differential expression tests are conducted (e.g. Wilcoxon rank sum) between each individual cluster and the other collective clusters. The upregulated differentially expressed genes could be considered positive markers and downregulated genes negative markers.
  
  > **Comments:**
  > **username_0**: What do you mean upregulated and and downregulated? I do not understand about them? Also, the 200 genes I mentioned, basically we cannot say those genes are marker genes for cluster A?  
  
  ---
  
  ### Answer by username_2 on 2024-11-06. Score: 1
  
  May I reignite this conversation? I don't really want to start a new topic for this because it's closely related to the op's question and the answers.
  
  What if you do the wilcoxon/MAST etc statistical tests for the clusters and look for a marker in a speicifc cluster. Let's say CD4 in cluster X. Cluster X doesn't have CD4 as statistically significant (so p\_adj > 0.05), OR you biologically you would exprect cluster X as a CD4 positive population but that statistical test lists CD4 as a statistically significant negative marker BUT with -0.1 log2FC.
  
  Where would you categorize cluster X in these 2 cases? (1.)not coming up as a significant DEG 2.) significant but with minimal negative log2FC although you expect it as positive side note: percent of cells expressing the given marker is very close in clusterX vs everything else.)
  
  Thanks in advance.
  
  > **Comments:**
  > **username_3**: Is this an actual answer or a follow up question/request for clarification of the original question?  
  > **username_2**: I intended this as a follow up question. OP asked basically what is a positive and a negative marker. Answers stated that we can look at positive LFC significant DEGs as positive, and negative LFC significant DEGs (from differential gene expression analysis, like FindAllMarkers used in seurat package). And i brought up the scenario i am interested to know the answer for. Maybe it can be it's own thread but i thought i try this way, idk.  
  
  ---
  
  ### Answer by username_4 on 2021-06-10. Score: 0
  
  A positive marker is a gene that is overexpressed in a cell population compared to other populations.
  
  A negative marker is a gene that is underexpressed in a cell population compared to other populations.
  
  I think the Seurat FindMarkers function has an option to output Log2FoldChange as well as the marker names. In this case the positive markers will have a positive Log2FoldChange, and the negative markers will have a negative Log2FoldChange.
  
  Both positive and negative markers can be used to describe a cell population. In the research that I've done in the past, there's a particular type of dendritic cell that is only distinguished from another dendritic cell type based on cell surface markers that it *doesn't* have; our own name for these DCs was "Triple negative".
  
  
  ---
  
  