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Example data walkthrough
A walkthrough for the updated SLiMEnrich app will be added here. In the meantime, visit the Shiny server, or:
- Clone the GitHub repository or download the release code.
- Make sure RStudio is installed, then double-click on
SLiMEnrich.Rprojto open the SLiMEnrich project.
- Open the
server.Rfile in RStudio and Run App.
Adenoviridae Example Data
This tutorial uses PPI data from the
data/ directory. Run SLiMEnrich and follow steps in Fig 1.For this example analysis, we have selected ELMc-Domain strategy.
Fig 1. Running example data.
1. Uploaded Data Tab
Uploaded Data tab shows content of the uploaded files (Fig 2). For this example, following default data is loaded:
- Adenoviridae PPIs
- Known instances of ELMs
- DMIs (retrieved from ELM)
- Pfam Domains (parsed from Uniprot)
Files are available in
data/ directory. (Fig 2)
Fig 2. Default files loaded for Adenoviridae analysis.
2. Potential DMIs Tab
This tab shows all possible interactions of mProteins and dProteins mediated by SLiMs (Potential DMIs). A total of 18 potential DMIs (11 Non-redundant) were predicted for adenoviridae family. These DMIs represents overall pool of the DMIs, ignoring the actual PPI data.
Results can be downloaded as .csv file through the download button (Fig 3).
Fig 3. Potential DMIs tab shows all possible DMIs.
3. Predicted DMIs Tab
This tab shows actual DMIs predicted in a PPI dataset. Out of 7 potential DMIs, 5 (4 Non-redundant) DMIs were found to be present in the PPI data. Results can be downloaded as .csv file through the download button (Fig 4).
Fig 4. Predicted DMIs tab shows DMIs captured by PPIs.
4. Summary Tab
This tab shows number of unique mProteins, motifs, domains and dProteins involved in predicted DMI dataset in the form of a bar char. A total of 3 unique mProteins interacted via 4 unique motifs with 4 unique domains of 5 dProteins (Fig 5).
Fig 5. Summary Statistics. Summary bar chart showing unique number of proteins, motifs and domains involved in predicted DMIs (mouse hover on plot bars to see the numbers).
5. Histogram Tab
Histogram tab shows enrichment in the form of a histogram marking observed and P-values. The observed value is 5 and empirical p-value is 0.002. Histogram might take couple of minutes to return results depending on the data size (Fig 6).
Fig 6. Histogram tab shows histogram, its summary and settings to change the look of the plot
This shows the frequency and proportion of ELMs involved in the predicted DMIs. LIG_Rb_pABgroove_1 and LIG_Rb_LxCxE_1 are more frequently involved in the adenoviridae DMIs. (Fig 7).
Fig 7. An interactive chart to show the distribution of ELMs in the predicted DMIs.
This shows the frequency proportion of Domains involved in the predicted DMIs. Retinoblastoma-associated protein B domains (PF01857 & PF01857) are more frequently involved in the adenoviridae DMIs. (Fig 8).
Fig 8. An interactive chart to show the distribution of Domains in the predicted DMIs.
8. Network Tab
Network tab shows DMI network of predicted DMIs (Fig 9).
Fig 9. Network tab shows DMI network in different layouts. A circular layout is shown where mProtein=red, motif=yellow, domain=purple and dprotein=blue