cluster identification and DEGs in single cell data
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14 days ago

Hello everyone I am working on single cell data (multiple samples) in which samples are grouped based on the condition (control and treated). For the data analysis, I have been using seurat package for pre-processing, normalization (SCT) and identified multiple clusters. Later, for each cluster, performed "DEGs" analysis based on the condition. From DEGs list, I found that the same gene is differential expressed in multiple cluster. Example : Gstm1 was identified in all three clusters as differential expressed gene during comparison of control and treated. Another gene Acaa1b was found as DEG in 2 clusters.

        Cluster 0   Cluster 1   Cluster 2
"Gstm1"     1   1   1
"Acaa1b"    1   1   0

Is it normal in single cell data to identified same gene (significant differential expressed) in multiple clusters?

Please let me know if I am doing something wrong.

deg cluster seurat analysis • 156 views
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It's normal since many genes are expressed in multiple cell types.

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Thanks for the confirmation :)

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