Boxplots


Differential Expression Results


*Displayed values are FDR adjusted p-values obtained from limma.
*Refer to following paper for more information:

Differential Expression Results


Long COVID-19 Protein Expression Explorer Documentation

The proteomic data has been generated using the OLINKs platform. For more information, refer to the following paper:

Proteomic blood profiling in mild, severe and critical COVID-19 patients

** If using information from this app for your research, then please cite the above paper.**

Summary of data demographics

A summary of the data demographics is:

  • 87 samples (after QC)
    • 28 Controls
    • 26 Cases - Mild symptoms
    • 9 Cases - Severe symptoms (typical symptoms)
    • 24 Cases - Critical symptoms (in ICU)
  • 4 OLINKS arrays (total 355 proteins after QC ):
    • Olink CARDIOVASCULAR II(v.5006)
    • Olink IMMUNE RESPONSE(v.3203)
    • Olink INFLAMMATION(v.3022)
    • Olink NEUROLOGY(v.8012)
  • Differential expression analysis was performed in R using the limma package. Age, gender, days since symptom onset and symptom severity (mild, severe, critical) were used as covariates.

Protein Expression Explorer user guide

The protein explorer is used by selecting the protein of interest by either its:

  1. Uniprot ID
  2. Protein symbol
  3. OLINK ID

Selecting a protein will plot the expression of the protein across the four disease symptom groups. The differential expression (DE) results for the selected protein across several different analyses is provided below the plot.

The following analyses were performed and can be selected using the checkbox in “Optional: select DE analysis results to show (multiple can be selected):”:

  1. “Covid_vs_Long_Covid”
    • DE between the covid group and long covid group
  2. “Control_vs_Long_Covid”
    • DE between the control group and long covid group
  3. “Control_vs_Covid”
    • DE between the control group and covid group

Differential Expression Results

The complete differential expression results for all analysis can be found under this tab.

Explanation of DE Results

The columns of the DE results are as follows:

  1. Analysis:
  2. Assay
    • This is the OLINK panel the protein originated from. Some proteins were present on multiple panels, e.g IL6.
  3. OLINK.ID
    • This is the OLINK specific protein ID
  4. Protein.ID
  5. Uniprot.ID
  6. logFC (95% CI)
    • Estimate of the log2-fold change with 95% confidence interval
  7. P.Value
    • raw p-value
  8. FDR.P.value
    • FDR adjusted p-value

Note

  1. Expression values are measured using the OLINK's arbitrary Normalized Protein eXpression (NPX) value, which is presented on the log2 scale, where a 1 NPX difference means a doubling of protein concentration.
  2. NPX values can be compared only for the same protein across the samples analysed.
  3. NPX values for 2 different analytes/proteins are not directly comparable.

Contacts

If you have any queries in regards to this app, then please contact:

ROSALIND: This app is hosted on the research computing facility at King's College London, Rosalind (https://rosalind.kcl.ac.uk), which is delivered in partnership with the National Institute for Health Research (NIHR) Biomedical Research Centres at South London & Maudsley and Guy's & St. Thomas' NHS Foundation Trusts, and part-funded by capital equipment grants from the Maudsley Charity (award 980) and Guy's & St. Thomas' Charity (TR130505).