text: user12477: 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?
  
  user104: 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.
  
original_text: 12477: <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>
   104: <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>
  