ibiomic

Analysis Method:

Due to the small number of samples, which prevents statistically significant results, a pairwise comparison of all sample pairs was conducted. Sample-vs-sample scatterplots are shown in Fig. 1.

Quality Estimation:

• Similarity:

  • Samples 1 and 2 show high similarity.

  • Samples 3 and 5 also show high similarity.

  • Sample 4 is similar to samples 3 and 5 but has an additional cluster of highly expressed genes.

• Interpretation:

  • This additional cluster suggests that sample 4 is similar to samples 3 and 5, but with some cells of another type.

  • Gene ontology analysis of the additional cluster reveals muscle-related genes (see Table 1), indicating possible muscle tissue contamination in sample 4.

Differences Between Treated and Non-Treated Tissues:

• Comparative Analysis:

  • Treated samples (1 and 2) show upregulation of genes related to the extracellular matrix.

  • Treated samples show downregulation of genes related to the immune response (see Tables 2 and 3).

Analysis Method:

Differentially expressed genes are detected as having high fold change (>2) and low p-value (<0.003) using 2-sample t-test. 

Quality Estimation:

• Quality control by calculating similarity index between samples has not revealed unexpected discrepancies (high similarity within each group, low similarity between groups). 

Differences Between Treated and Non-Treated Tissues:

• Comparative Analysis:

  • Group 2 vs group 3 comparison reveals up-regulation of genes related to immune process,  which are also upregulated in group 1 vs group 3 but  less significantly (Fig. 1a and 1b, list of genes in table 1).

  • Extracellular-process-related genes are down-regulated in group 1 vs group 2 (Fig 2a, table 2).

  • Violin plots (Fig. 2a) visualize expression of one gene from both gene clusters -"immune" and "extracellular process" related clusters. Any other genes can be plotted in similar way on demand.

  • Based on this analysis and group labels it can be concluded that investigated sickness up-regulated immune-related genes. Treatment diminishes them toward healthy state, however, it also down-regulates expression of extracellular-process-related genes.