Genomic signatures, sometimes expressed as a weighted sum of genes, are an algebra over genes.

In Brief

  • Genomic signatures:

    • a list of genes

    • weighted gene(s)

    • an algebra over genes

  • Example of interpretation

    • data from a publication1.

    • gene signature

      • =FN1 + VIM + ZEB1 + ZEB2 + TWIST1 + TWIST2 + SNAI1 + SNAI2 + CDH2 - CLDN4 - CLDN7 - TJP3 - MUC1 - CDH1

Protocol

  • Click on VIEW MY DATA and Select Data File.

  • Choose local file CMS_subtypes.txt.

  • Choose Phenotypic data: categories or non-genomic in a rectangle (e.g. age, mutation status: 'wt' or 'mutant').

  • Choose The first column is sample IDs.

  • Choose There is other public data in Xena on these samples (e.g. TCGA) and want to connect to it..

  • Choose Search for study TCGA Colon and Rectal Cancer (COADREAD).

  • Click on IMPORT and FINISH.

    step 1

  • Back to VISUALIZATION.

  • Click Search Phenotype to add Phenotype CMS_subtype.

  • Add a new column and choose gene expression: =FN1 + VIM + ZEB1 + ZEB2 + TWIST1 + TWIST2 + SNAI1 + SNAI2 + CDH2 - CLDN4 - CLDN7 - TJP3 - MUC1 - CDH1.

  • Final input.

    step2

  • Choose Chart & Statistics of Column C or Column D to generate figures.

    figure

In summary, the present study proposed that taxonomy of four consensus molecular subtypes (CMS) of colorectal cancer(CRC) reflected significant biological differences in the gene expression-based molecular subtypes.

  1. Nat Med. 2015 Nov;21(11):1350-6. doi: 10.1038/nm.3967. ↩︎