Boxplots
Differential Expression Results
*Displayed values are FDR adjusted p-values obtained from limma.
*Refer to following paper for more information:
Differential Expression Results
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 and days since symptom onset were used as covariates.
Protein Expression Explorer user guide
The protein explorer is used by selecting the protein of interest by either its:
- Uniprot ID
- Protein symbol
- 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):”:
- “Control_v_Case”
- DE between the control groups and cases (mild, severe, and critical group are merged into cases)
- “Control_v_Mild”
- DE between the control group and the mild symptom group
- “Control_v_Severe”
- DE between the control group and the severe symptom group
- “Control_v_Critical”
- DE between the control group and the critical symptom group
- “Mild_v_Severe”
- DE between the mild group and the severe symptom group
- “Mild_v_Critical”
- DE between the mild group and the critical symptom group
- “Severe_v_Critical”
- DE between the severe group and the critical symptom group
- “Longitudinal_in_Mild”
- DE in the 6 patients with mild symptoms taken at two different time points
- “Longitudinal_in_Critical”
- DE in the 5 patients with critical symptoms taken at two different time points
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:
- Analysis:
- Assay
- This is the OLINK panel the protein originated from. Some proteins were present on multiple panels, e.g IL6.
- OLINK.ID
- This is the OLINK specific protein ID
- Protein.ID
- Uniprot.ID
- logFC (95% CI) b9ikllk
- Estimate of the log2-fold change with 95% confidence interval
- P.Value
- raw p-value
- FDR.P.value
- FDR adust p-value
Note
- 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.
- NPX values can be compared only for the same protein across the samples analysed.
- 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:
- Dr. Hamel Patel hamel.patel@kcl.ac.uk
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).