1. Introduction

  • A general workflow of RNA data analysis consists of the following steps
  1. Explore your samples
  • Unbiased unsupervised clustering
  • PCA, tSNE, UMAP
  • Toplister
  • Genes that do make a difference in this set
  • Goals
    • Data check; bias?
    • Groups?
  1. Explore differences between groups
  • Differential expression
  • Specific (groups of) genes
  1. Explore patterns
  • Overrepresentation
    • Gene Ontology
    • Pathways
  1. Explore relations
  • Generate a signature
  • Compare with other signatures

2. Finding drug responsive pathways in RA

Data used:

  • Exp Rheumatoid arthritis tocilizumab - Takeshita - 22 - deseq2_rlog - gse113156
  • 22 samples taken before and after tocilizumab treatment of CD4 and CD8 T cell in rheumatoid arthritis patients

Techniques used:

  • RNA Seq

References

2.1. Explore your samples

Analyses used

  • PCA

2.1.1. Clustering with PCA analysis

2.1.2. Clustering with tSNE maps

We’ve seen that the expression of genes differs among the samples and some types of tumors seem to specifically express certain genes. To further explore the type of data we’re dealing with, an unbiased unsupervised type of clustering analysis is a good idea. One recently developed algorithm is the tSNE map.

  • Click the button below to show the tSNE map in R2


  • Colors are not set by default, under ColorMode select Color by Track and use the itcc_model track, click Next to show the changes

2.2. Explore differences between groups

2.3. Explore patterns

2.4. Explore relations

3. Determine a lineage specific RA signature

Data used:

  • Disease Rheumatoid arthritis (MTX) monotherapy - Okuzono - 336 - deseq2_vst - gpl17303
  • 337 samples of T cells in each developmental stages in healthy volunteers and patients with rheumatoid arthritis

Techniques used:

  • RNA Seq

References

3.1. Explore your samples

Analyses used

  • t-SNE: t-distributed stochastic neighbor embedding statistics

3.2. Explore differences between groups

3.3. Explore patterns

3.4. Explore relations