[paper] Bioinformatics screening of biomarkers related to liver cancer

 

https://doi.org/10.1186/s12859-021-04411-1

 

 

0. TCGA DB : Ready data

 

1. DESeq2 : Upregulated and Downregulated genes.

- |logFC| > 2 , FDR < 0.05

 

2. GSEA : Enrichment (GO) and Pathway (KEGG, Reactome) analysis.

- FDR(GO) < 0.01 , P-value(KEGG) < 0.05

 

3. STRING DB and Cytoscape : PPI network hub for key genes.

- top 15 hub genes

 

4. Oncomine (gene chip) DB : Differential expression analysis and meta-analysis to confirm key genes.

 

5. Validation : Decision trees, random forests, SVM

 

6. KM-plotter DB : Survival analysis to confirm key genes.