Tools and instructions

Introduction
This page contains additional information to support the TCGA PanCanAtlas Stemness project. We provide two components:
Stemness Index Workflow provides the steps and methods to regenerate mRNA and mDNA-based stemness scores and create Stemness Indexes of TCGA tumor samples (mRNAsi and mDNAsi). This workflow also provides steps to generate corresponding stemness indices for non-TCGA samples (e.g., users own samples). PanCanStemness Web portal contains the enrichment analysis reported in our study.

Stemness Index Workflow
This workflow describes the steps we developed to generate our Stemness Indices (mRNAsi and mDNAsi).

The step-by-step explanation includes:
a) how to download stem/progenitor cells from the Progenitor Cell Biology Consortium(PCBC),
b) download TCGA PanCanAtlas datasets,
c) train a stemness signature using normal stem cells,
d) apply the one-class algorithm to define a stemness index for each tumor sample.

Users can replace TCGA PanCanAtlas dataset with their own samples to derive the corresponding Stemness Indices.
Gene expression-based index
DNA methylation-based index

Article
Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.
Malta et al., 2018, Cell 173, 338–354
VIDEO ABSTRACT
ONLINE
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