Table of Contents

  1. Explore the Collection by Study
  2. Visualize the Top-Occurring Molecules
  3. Perform GSVA with Sepsis Signatures
  4. Perform Pathway Enrichment
  5. General Troubleshooting

SeptiSearch welcome page.

Expore the Collection by Study

This tab allows you to easily browse and search the data we’ve curated.

Select a study from the table to display all associated molecules.

Visualize the Top-Occurring Molecules

The second tab provides a more visual way of search the curated signatures, with a greater focus on the molecules frequently occuring within SeptiSearch.

The plot shows the most common molecules in the dataset for the indicated time point, with the sidebar on the left providing a number of ways to filter the data. The “Restore defaults” button at the bottom of the sidebar will reset all inputs, returning the plot to its original state.

Hover over a column in the plot to see the details for that molecule.

You can click one of the bars (molecule & timepoint specific) in the plot to show all entries for that molecule in SeptiSearch, and download this table using the button at the bottom of the sidebar

Perform GSVA with Sepsis Signatures

Successfully loaded user data for GSVA.

If you’d like to submit your own data for GSVA, the expression component needs to meet the following criteria:

While you can submit only the expression data for GSVA, it’s recommended to also include metadata (e.g. sample groups) to make the final heatmap more informative. There are a few requirements for submitted metadata:

Once you’ve uploaded either the expression data alone, or expression and metadata, select “Submit expression data for GSVA” to run the analysis and view the results, which include a summary table and heatmap. Explanations of all the columns can be viewed by hovering over the column names with your cursor.

Results from SeptiSearch's GSVA implementation.

The full results table can be downloaded with the button at the bottom of the sidebar, and the image can be saved by right-clicking on it and selecting “Save Image…” from the context menu.

Perform Pathway Enrichment

SeptiSearch features the ability to upload a list of your own genes(e.g. those identified as differentially expressed in an RNA-Seq experiment) and test them for enriched Reactome pathways using ReactomePA, as well as Hallmark gene sets and GO terms via enrichR. This functionality is designed to complement the use of GSVA, which tests your data for the dysregulation of our curated sepsis signatures.

Inputting data for pathway enrichment.

Top table of enrichment results, from ReactomePA.

Lower table of enrichment results for enrichR.

Just like the “GSVA” tab, we have provided an example list of genes, based on one of our sepsis signatures (Xiong et al):

General Troubleshooting

If you run into problem or encounter bugs while using SeptiSearch, try resetting the inputs to their original state (e.g. for the Explore Data by Study and Visualize Molecule Occurence tabs), or refresh your browser window to reload the app. If the problem persists, you can submit an issue on our Github page by following this link.

If you encounter a problem with the Perform GSVA with Sepsis Signatures and Perform Pathway Enrichment tabs, please ensure your inputs match all the specified criteria for each tab before reporting the problem via a Github issue.