Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray

STAR Protoc. 2023 Sep 15;4(3):102509. doi: 10.1016/j.xpro.2023.102509. Epub 2023 Aug 11.

Abstract

Here, we present a protocol for deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray. We describe steps for utilizing NMF-defined group 3/group 4 metagenes to calculate a continuum score between 0 and 1 that can be projected onto new sample data analyzed via RNA-sequencing. We then detail procedures for reverse engineering a continuum score for samples analyzed via DNA methylation microarray using a random forest classifier.

Keywords: Bioinformatics; Cancer; Molecular Biology; RNAseq; Sequence analysis; Sequencing.

MeSH terms

  • Base Sequence
  • Cerebellar Neoplasms* / diagnosis
  • Cerebellar Neoplasms* / genetics
  • Cerebellar Neoplasms* / pathology
  • DNA Methylation / genetics
  • Humans
  • Medulloblastoma* / diagnosis
  • Medulloblastoma* / genetics
  • Medulloblastoma* / pathology
  • RNA

Substances

  • RNA