1. I searched for (...) and didn’t get any results.
  2. I used the “Analyse gene expression” tool with my mouse proteomics data set. I notice that the database is based on human pathways – does the software automatically convert my mouse gene names to the human orthologs? Or can’t I use the software for mouse?
  3. I am having trouble installing a local Reactome Neo4J server.
  4. Does Reactome contain pathway information from non-human species?
  5. Explain the identifiers associated with entities and events.
  6. The analysis report includes lists of significantly up- and down-regulated single genes. Which statistical analysis does the software use for these values?
  7. Where can I find earlier versions of the Reactome database?
  8. Can I visualize gene expression data (color nodes) according to gene expression level with Reactome?
  9. I have a list of input genes. I want to retrieve all the pathways in which the genes are involved. How can I do this using a Neo4j Cypher query?
  10. How can I find all pathways reported for one organ? For example, I want to extract all reported pathways in (tissue X) for (species Y).
  11. After submitting a list of genes for Reactome Analysis, how do I download the fully expanded 'Event Hierarchy' list on the left side of the screen?
  12. I have a proteomics data set that I would like to use for quantitative pathway analysis. Is there training material available to help me?
  13. Is there an API for Reactome? Can I do pathway analysis through the API?
  14. I have a list of Reactome pathway IDs. I want to find whether any of them are disease pathways and also retrieve associated disease names. Is it possible to retrieve the information using API or neo4j graph database query?
  15. Is there a mapping file between KEGG and Reactome pathways?
  16. Is it possible to know how many of my uploaded genes are found within each specific hierarchical pathway category identified in the Reacfoam view? For instance, how many of my genes belong to pathways that would be included in the "Immune" category, etc.
  17. Can I submit a list of differentially expressed genes, as log2 fold change values, coming from two different conditions to have a quantitative representation of pathways involvement? If yes, how can I prepare and submit my file?
  18. Should I use the gene symbol or the NCBI identifiers to make requests to the identifiers endpoint of the Analysis Service?
  19. I need to do a network analysis for (species) from RNA seq data. Can you please guide me on how to generate an FI network?
  20. How can I use Neo4J to identify all the genes for a given pathway?
  21. Is there a way to download high level images which can be zoomed in locally (after download)?
  22. Is it possible to download the inferred pathways for mouse (or another species), similar to the GMT file for human pathways on the downloads page?
  23. Is there a permanent link available for my analysis results?
  24. I submitted a list for expression analysis using the PADOG or CAMERA tools and the output Excel file with the statistics is missing a lot of significant genes. What is the explanation for this?
  25. Can I do pathway analysis using R?
  26. Can I submit a list of differentially expressed genes, as log2 fold change values, coming from two different conditions to have a quantitative representation of pathways involvement?
  27. Is it possible to directly connect my protein protein interaction network with the Reactome database or do I have to extract the required data and separately build the graph?