Plasma Proteomics-Olink® Explore HT

NPX, Normalized Protein eXpression, is Olink’s arbitrary unit which is in Log2 scale. Following sequencing, the raw data is converted to counts, assigning an integer value to each assay-sample combination based on the detected copy numbers. These raw data counts are converted into NPX values, enabling the identification of protein level changes within different sample sets, and establishing protein signatures. In general, a higher NPX value refer to a higher protein concentration.

The x-axis represents the sample names. The y-axis represents the NPX values. A red bar indicates a QC warning sample, and a blue bar represents QC pass sample.

Principal component analysis (PCA) is a statistical technique for analyzing large dataset by reducing the dimensionality of the dataset. In this analysis, PCA is conducted on the NPX data file, and all samples are plotted as a scatterplot along the selected principal components. It can be useful for showing that samples separate, or cluster based on variables of interest. In addition, it can be used to identify potential outlier samples.

Dots in different colors represent different groups. The closer the distance between samples, the higher the similarity between samples.

Hierarchical clustering is a method used to get an overview of data, and to identify subgroups of similar samples or proteins based on protein profiles. This analysis is often visualized through a heatmap, where similar proteins or samples are positioned adjacent to each other. The protein expression levels are then represented using a color gradient on the heatmap.

Red color indicates proteins with higher NPX expression levels, and blue color indicates proteins with lower NPX expression levels. The color ranging from red to blue indicates that NPX values range from large to small.

The comparison of protein expression level among groups are performed using t-test or ANOVA and the result is visualized using volcano plot.

The x-axis shows the NPX.difference between two groups, and the y-axis shows the -log(p-value) value(base 10). NPX.different= NPX.group1 – NPX.group2. Red dots represent significant differential expressed protein. Blue dots represent insignificant differential expressed proteins.

GO is the abbreviation of Gene Ontology (http://www.geneontology.org/), which is a major bioinformatics classification system to unify the presentation of gene properties across all species. It includes three main branches: cellular component, molecular function, and biological process. GO terms with padj < 0.05 are significant enrichment.

The x-axis represents the GO Term, and the y-axis indicates the level of significance of enrichment for each GO Term, expressed as -log10(padj). Different functional categories are represented by varying colors.