Table 2. TCGA gene expression results.
| Rank | SLPR | MGSA | geneSetTest |
|---|---|---|---|
| 1 | REACTOME_APOPTOTIC_CLEAVAGE_OF_CELL_ADHE... | KEGG_SPLICEOSOME | REACTOME_CELL_CYCLE_MITOTIC |
| 2 | PID_DELTA_NP63_PATHWAY | KEGG_LYSOSOME | REACTOME_CELL_CYCLE |
| 3 | +KEGG_MATURITY_ONSET_DIABETES_OF_THE_YOUN... | REACTOME_SIGNALING_BY_RHO_GTPASES | REACTOME_DNA_REPLICATION |
| 4 | REACTOME_GAP_JUNCTION_TRAFFICKING | REACTOME_HEMOSTASIS | REACTOME_MITOTIC_M_M_G1_PHASES |
| 5 | +KEGG_COMPLEMENT_AND_COAGULATION_CASCADES | KEGG_RIBOSOME | REACTOME_MITOTIC_G1_G1_S_PHASES |
| 6 | +PID_HNF3A_PATHWAY | REACTOME_GENERIC_TRANSCRIPTION_PATHWAY | REACTOME_S_PHASE |
| 7 | REACTOME_DNA_REPLICATION | PID_P53_DOWNSTREAM_PATHWAY | REACTOME_G1_S_TRANSITION |
| 8 | KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCH... | KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_ME... | REACTOME_MITOTIC_PROMETAPHASE |
| 9 | PID_AURORA_B_PATHWAY | REACTOME_METABOLISM_OF_VITAMINS_AND_COFA... | REACTOME_SYNTHESIS_OF_DNA |
| 10 | REACTOME_COLLAGEN_FORMATION | KEGG_CELL_ADHESION_MOLECULES_CAMS | KEGG_CELL_CYCLE |
| 11 | +REACTOME_REGULATION_OF_COMPLEMENT_CASCAD... | REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT | REACTOME_CELL_CYCLE_CHECKPOINTS |
| 12 | PID_MYC_ACTIV_PATHWAY | KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRA... | REACTOME_M_G1_TRANSITION |
| 13 | PID_REG_GR_PATHWAY | KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACT... | REACTOME_PROCESSING_OF_CAPPED_INTRON_CON... |
| 14 | +REACTOME_O_LINKED_GLYCOSYLATION_OF_MUCIN... | REACTOME_CELL_CYCLE_MITOTIC | REACTOME_MRNA_PROCESSING |
| 15 | +REACTOME_BILE_ACID_AND_BILE_SALT_METABOL... | KEGG_ARGININE_AND_PROLINE_METABOLISM | REACTOME_METABOLISM_OF_RNA |
| 16 | PID_TAP63_PATHWAY | PID_AR_PATHWAY | REACTOME_DNA_STRAND_ELONGATION |
| 17 | +KEGG_LYSOSOME | KEGG_AXON_GUIDANCE | REACTOME_HIV_INFECTION |
| 18 | REACTOME_CELL_CYCLE_MITOTIC | KEGG_PEROXISOME | KEGG_DNA_REPLICATION |
| 19 | REACTOME_GAP_JUNCTION_ASSEMBLY | KEGG_ARACHIDONIC_ACID_METABOLISM | REACTOME_REGULATION_OF_MITOTIC_CELL_CYCL... |
| 20 | PID_E2F_PATHWAY | PID_TELOMERASE_PATHWAY | REACTOME_DNA_REPAIR |
| 21 | PID_FANCONI_PATHWAY | REACTOME_RNA_POL_III_TRANSCRIPTION | PID_ATR_PATHWAY |
| 22 | REACTOME_KINESINS | KEGG_RNA_DEGRADATION | REACTOME_CHROMOSOME_MAINTENANCE |
| 23 | PID_FOXM1_PATHWAY | REACTOME_ADAPTIVE_IMMUNE_SYSTEM | REACTOME_G2_M_CHECKPOINTS |
| 24 | +NABA_ECM_AFFILIATED | KEGG_BIOSYNTHESIS_OF_UNSATURATED_FATTY_A... | REACTOME_ORC1_REMOVAL_FROM_CHROMATIN |
| 25 | +PID_AR_TF_PATHWAY | PID_DELTA_NP63_PATHWAY | REACTOME_ASSEMBLY_OF_THE_PRE_REPLICATIVE... |
Top 25 MSigDB v5.0 C2.CP gene sets selected by the SLPR, MGSA and geneSetTest methods for an analysis of the TCGA RNAseq data for lung adenocarcinoma and lung squamous cell carcinoma samples. For the SLPR results, a ‘+’ before the gene set indicates enrichment in lung adenocarcinoma versus lung squamous cell carcinoma, i.e. the gene set members have larger expression values in lung adenocarcinoma versus lung squamous cell carcinoma.