GSVA was applied to explore differences in enrichment scores between low-risk and high-risk groups, using pathways from the Molecular Signatures Database (MSigDB) hallmark set as a reference. GSEA was also performed for each lncRNA of the 10 CuRLs. The correlation between the expression of each lncRNA and other genes was computed. Gene lists were sorted by the value of correlation and then GSEA was performed based on KEGG pathway database with P value cutoff set to 0.05. Protein-coding genes co-expressed with the 10 CuRLs were identified using |Pearson correlation coefficient| >0.5 and P<0.001 as the cut-off. GO and KEGG functional enrichment analyses were carried out to understand the functions of these correlated mRNAs. These analyses were conducted mainly based on R packages ‘GSVA’, ‘msigdbr’, ‘clusterProfiler’ (22 (link)), ‘org.Hs.eg.db’, and ‘enrichplot’.
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Exploring lncRNA-driven Pathways in Cancer
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Curls
Gene
Lncrna
Mrnas
Protein genes
Risk groups
Corresponding Organization :
Other organizations : Ruijin Hospital, Shanghai Jiao Tong University
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Variable analysis
independent variables
- Low-risk group
- High-risk group
- Enrichment scores of pathways from the Molecular Signatures Database (MSigDB) hallmark set
- Correlation between the expression of each lncRNA and other genes
- Protein-coding genes co-expressed with the 10 CuRLs
- Pathways from the Molecular Signatures Database (MSigDB) hallmark set
- KEGG pathway database
- Pearson correlation coefficient threshold (|Pearson correlation coefficient| >0.5 and P<0.001)
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