1 Sample Information

Analysis from the results of a label free mass spectrometry experiment on paraffin embedded samples stratified as follows:

1.1 First Batch of Samples

  • Red Blood Cells rich clot analogues (RBC): n = 3
  • Fibrin rich clot analogues (FIB): n = 4

1.2 Second Batch of Samples

  • Red Blood Cells rich clot analogues (RBC): n = 5
  • Fibrin rich clot analogues (FIB): n = 5

The Venn Diagram generated using the overlapping proteins between the two data sets shows that 73 proteins are overlapping between the RBC (Set_1) and FIB (Set_2) Groups - and this intersection is used for comparison between groups, 67 proteins are unique to the RBC samples, and 43 proteins are unique to the FIB samples.

2 RBC Analysis

2.1 Pearson correlation

Using the correlation matrix above to extract information on the abundancy profile of the top 50 highly correlated proteins with a threshold of +/- 0.80, the network analysis was carried out and resulted in the graph below. The node size is proportional with the degree (how connected the protein is), the red edges represent positive correlation and blue edges represent negative correlation. The optimal community structure was calculated for the graph, in using the maximal modularity score.This analysis resulted in the communities represented as the node colours and shown in the table below.

##Network Analysis





3 FIB Analysis

3.1 Pearson correlation analysis

3.2 Network analysis

4 Differential Analysis

Here I used a linear model approach to assess differential abundance/expression between the two groups - this analysis resulted in 32 differentially abundant proteins. The table below show the metrics of the top-ranked proteins from the linear model fit. The data was pre-processed with log-transformation and quantile normalisation to ensure that the expression distributions of each sample are similar across the entire experiment and not skewed.

5 Pathway Enrichment Analysis

Pathway enrichment analysis were conducted on differentially abundant proteins related RBC and FIB using the InterMineR R package. Here the pathways were tested for over-representation in each of the proteins with fold change related with RBC and FIB relative to what is expected by chance and a p-value is computed for each pathway. The plots below represent the top 10 enriched pathways for the aforementioned communities - you can hover the bars for p-value information.