AMP PD Targeted Proteomics Differential Expression at Baseline
Analysis Methodology
Note: The analysis that produced this target list is available to all registered AMP PD users in Terra and can be reused in your work.
Introduction
This analysis uses proteomics data described here.
Differential expression
Cohorts for DE were created by filtering for visit month = 0 and condition = case or control.
Tools:
- R
- Olink Analyze Package
- olink_ttest
Input:
Underlying Analyses
Differential expression/T-test
Protein
Targeted proteomics data generated using the Olink Explore platform was analyzed using Olink provided analysis scripts within Terra. Data from release v3 was utilized, however, the data was reformatted by combining the separate Olink Explore panels into one file. Data has been uploaded into a community workspace google bucket for use. The proteomics data frame was combined with demographics and case/control info and was filtered to only contain samples at baseline for control and disease. The two groups compared were “Control” and “Case.” The Olink ttest function was utilized and it performs a Welch 2-sample t-test at confidence level .95 for every protein within a given grouping variable. The function corrects for multiple testing using Benjamini-Hochberg (“fdr”).
CSF, Plasma
Proteomics
Parkinson's Disease Biomarkers Program (PDBP), Parkinson's Progression Markers Initiative (PPMI)
Data Dictionary
| Field Name | Field Name Expanded | Short Description (optional) |
|---|---|---|
| Assay | Assay name | Olink protein assay for proximity extension assay |
| OlinkID | Unique Olink ID | Unique Olink ID |
| uniprot_id | Uniprot ID | Uniprot ID |
| ensembl_gene_id | ENSEMBL Gene ID | ENSEMBL Gene ID |
| Panel | Olink panel | Olink panel |
| estimate | Difference in mean NPX between groups | |
| Case | Case group | Average Expression for case group |
| Control | Control group | Average Expression for control group |
| 0 | Month zero time point | Average Expression for month zero time point |
| 48 | Month 48 time point | Average Expression for month 48 time point |
| statistic | Value of the t- statistic | |
| p_val | P value | P value for the test |
| parameter | Degrees of freedom for the t-statistic | |
| conf.low | Confidence low | Low bound of the confidence interval for the mean |
| conf.high | Confidence high | High bound of the confidence interval for the mean |
| method | Method that was used for analysis | |
| alternative | Description of the alternative hypothesis | |
| adj_p_val | Adjusted p value | Adjusted p value for the test (Benjamini & Hochberg) |
| Threshold | Text indication if assay is significant (adjust p-value < 0.05) | |
| Dataset | Dataset source | Data set source of D01 or D02 |
| Tissue | Tissue source | Sample tissue source: CSF or Plasma |
| Condition | Condition of the t-test: case or control | |
| gene_type | Gene type | Gene type from GENCODE |
| hgnc_symbol | HGNC symbol | HGNC symbol |