Representative gene sets within public databases related to our tMDS versus normal dataset (11 000 genes): GSEA
| Gene set name . | Genes in curated gene set . | Genes in our gene set . | ES . | FDR q value . | Description of gene set . |
|---|---|---|---|---|---|
| Myc-related | |||||
| LEE_MYC_UP | 54 | 30 | 0.49 | 0.023 | Genes Myc up-regulated in mouse and human hepatocellular carcinoma |
| FERNANDEZ_MYC_TARGETS | 180 | 105 | 0.41 | 0.008 | Regulatory and biologic diversity among Myc-target genes |
| MENSSEN_MYC_UP | 34 | 17 | 0.60 | 0.011 | Genes up-regulated by MYC in human umbilical vein endothelial cells |
| MYC_TARGETS | 42 | 20 | 0.57 | 0.008 | Regulatory networks of Myc-responsive genes |
| SCHUMACHER_MYC_UP | 54 | 30 | 0.52 | 0.011 | Multiple functions of Myc and its target genes |
| Translational | |||||
| BRENTANI_PROTEIN_MODIFICATION | 150 | 78 | 0.32 | 0.094 | Cancer-related genes involved in protein modification |
| MRNA_PROCESSING | 47 | 32 | 0.64 | 0.000 | Genes involved in mRNA processing (Broad Institute)* |
| MRNA_SPLICING | 58 | 32 | 0.51 | 0.012 | Genes involved in mRNA splicing (Broad Insitute)* |
| TRNA_ SYNTHETASES | 20 | 16 | 0.59 | 0.014 | tRNA synthetases (Broad Institute)* |
| RIBOSOMAL_PROTEINS | 123 | 39 | 0.78 | 0.000 | Genes curated by GenMapp2.1† |
| MRNA_PROCESSING_REACTOME | 121 | 66 | 0.53 | 0.000 | Genes curated by GenMapp2.1† |
| TRANSLATION_ FACTORS | 52 | 27 | 0.59 | 0.002 | Genes curated by GenMapp2.1† |
| Wnt-related | |||||
| KENNY_WNT_UP | 51 | 19 | 0.43 | 0.142 | Genes deregulated by Wnt in murine mammary epithelial cells |
| LIN_WNT_UP | 56 | 31 | 0.36 | 0.182 | Wnt target genes associated with MLL in human leukemia up-regulated in human colon cancer |
| Gene set name . | Genes in curated gene set . | Genes in our gene set . | ES . | FDR q value . | Description of gene set . |
|---|---|---|---|---|---|
| Myc-related | |||||
| LEE_MYC_UP | 54 | 30 | 0.49 | 0.023 | Genes Myc up-regulated in mouse and human hepatocellular carcinoma |
| FERNANDEZ_MYC_TARGETS | 180 | 105 | 0.41 | 0.008 | Regulatory and biologic diversity among Myc-target genes |
| MENSSEN_MYC_UP | 34 | 17 | 0.60 | 0.011 | Genes up-regulated by MYC in human umbilical vein endothelial cells |
| MYC_TARGETS | 42 | 20 | 0.57 | 0.008 | Regulatory networks of Myc-responsive genes |
| SCHUMACHER_MYC_UP | 54 | 30 | 0.52 | 0.011 | Multiple functions of Myc and its target genes |
| Translational | |||||
| BRENTANI_PROTEIN_MODIFICATION | 150 | 78 | 0.32 | 0.094 | Cancer-related genes involved in protein modification |
| MRNA_PROCESSING | 47 | 32 | 0.64 | 0.000 | Genes involved in mRNA processing (Broad Institute)* |
| MRNA_SPLICING | 58 | 32 | 0.51 | 0.012 | Genes involved in mRNA splicing (Broad Insitute)* |
| TRNA_ SYNTHETASES | 20 | 16 | 0.59 | 0.014 | tRNA synthetases (Broad Institute)* |
| RIBOSOMAL_PROTEINS | 123 | 39 | 0.78 | 0.000 | Genes curated by GenMapp2.1† |
| MRNA_PROCESSING_REACTOME | 121 | 66 | 0.53 | 0.000 | Genes curated by GenMapp2.1† |
| TRANSLATION_ FACTORS | 52 | 27 | 0.59 | 0.002 | Genes curated by GenMapp2.1† |
| Wnt-related | |||||
| KENNY_WNT_UP | 51 | 19 | 0.43 | 0.142 | Genes deregulated by Wnt in murine mammary epithelial cells |
| LIN_WNT_UP | 56 | 31 | 0.36 | 0.182 | Wnt target genes associated with MLL in human leukemia up-regulated in human colon cancer |
This list includes gene sets identified as strongly correlated Myc-, Wnt-, and translational-activated genes by GSEA. The 14 curated gene sets listed are highly enriched relevant datasets with FDR < 0.20. Enrichment score (ES) is a statistical measure reflecting the degree of correlation between genes within specific public datasets to those genes highly represented within the tMDS versus normal dataset. NES is an ES normalized for the size of the gene set.
The tMDS versus normal dataset was compared with curated database of gene sets published in the Molecular Signature Database (MsigDB; Broad Institute; http://www.broadinstitute.org/gsea/msigdb/index.jsp).
Gladstone Institutes, University of California at San Francisco, http://www.wikipathways.org/index.php.