Microglia Annotation Tool: a transcriptional subtype detector

FAQ

• How do I use the online tool ?

  Create a list of genes that are expressed in your microglia sample, or extract it from a source of interest (e.g. a publication, or a dataset).
  Select the species (human or mouse) and make sure the gene nomenclature is correct (e.g. “TREM2” for human, “Trem2” for mouse).
  
  The tool allows the upload of .csv & .tsv files, where it will search for a column named “gene” or “genes”, or if that isn't found it will take the first column in your file. Alternatively, you can type (or copy-paste) your list of line-separated or comma-separated genes in the text box. Once the list is uploaded or typed, click on "Run analyse". The tool will then analyze the data and provide you with a report.
  
  example file : example.txt, example.csv

• How long is my data stored ?

  The data is removed immediately after processing, regardless of whether the analysis was successful. The resulting report is kept for 3 months.

• How does the tool identify microglia subtypes?

  We have built a curated list of reference marker genes for each cell state, integrating data from 12 landmark microglia transcriptomics studies in AD across different samples. DEGs per study were ranked for each cell state according to the original publication, and were included in the reference list if they ranked in the top 100 DEGs of at least 2 studies. The input list of genes is intersected with all the cell states reference markers lists, and a percentage of overlap is calculated for every reference (intersection size / reference size) and plotted from highest to lowest overlap. Readers can explore further about microglia cell states and their annotation in our recent review (link will be added upon publication). The reference lists of genes for all human and mouse cell states can be downloaded at the link below.
  

  • mouse_microglia_cellstates_reference.xlsx
  • human_microglia_cellstates_reference.xlsx