Multi-omic insights in pediatric thyroid cancer

Multi-omic insights in pediatric thyroid cancer: germline predisposition, driver mutations, gene fusions, and transcriptional networks

Author

Gurpreet Kaur

Requirements

• R
• Rstudio

Code for the figures generated in the manuscript

• RNA-Seq differential gene expressions analysis. The corresponding expression heatmap of genes in which somatic and germline variants were identified in WES dataset. File: fig_A.Rmd

• RNA-Seq fusion analysis. Bulk RNA-Seq Fusion pipeline

  • a) Subtype-wise distribution of 86 fusions across six subtypes, allowing comparison of subtype-specific events. File: fig_B.Rmd

• Tumor vs. Normal differential gene expression analysis. File: fig_C.Rmd

  • a) PCA plot
  • b) Expression heatmap for 1687 DEGs (padj<0.05)
  • c) Volcano plot for 1687 DEGs
  • d) Heatmap for top 30 DEGs
  • e) Heatmap for 23 genes of interest
  • f) Volcano plot for 23 genes of interest

• Phenotype_Subtypes analysis. File: fig_D.Rmd

  • a) PCA plot among 6 subtypes
  • b) Upset plot for the five contrasts

• PTC vs. FTC differential gene expression analysis. File: fig_E.Rmd

  • a) Heatmap for 2081 degs (padj < 0.05)
  • b) Volcano plot for 2081 degs (padj < 0.05)
  • c) Expression heatmap for 23 genes of interest