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Table 1 List of cellular pathways enriched with genes within LOH regions

From: In silico analyses reveal common cellular pathways affected by loss of heterozygosity (LOH) events in the lymphomagenesis of Non-Hodgkin’s lymphoma (NHL)

Gene set name K Description k k/K* Pvalue
KEGG_Arginine_and_proline_metabolism 54 Arginine and proline metabolism 6 0.1111 4.84 × 10-4
Reactome_double_strand_break_repair 24 Genes involved in Double-Strand Break Repair 3 0.125 9.73 × 10-3
Microtubule_associated_complex 47 Genes annotated by the GO term GO:0005875. Any multimeric complex connected to a microtubule. 4 0.0851 1.13 × 10-2
PID_S1P_S1P3_pathway 29 S1P3 pathway 3 0.1034 1.64 × 10-2
Reactome_unwinding_of_DNA 11 Genes involved in Unwinding of DNA 2 0.1818 1.71 × 10-2
Biocarta_FAS_pathway 30 FAS signaling pathway (CD95) 3 0.1 1.80 × 10-2
Reactome_downregulation_of_ERBB2_ERBB3_SIGNALING 12 Genes involved in Downregulation of ERBB2:ERBB3 signaling 2 0.1667 2.03 × 10-2
KEGG_Non_homologous_end_joining 14 Non-homologous end-joining 2 0.1429 2.73 × 10-2
PID_IL5_pathway 14 IL5-mediated signaling events 2 0.1429 2.73 × 10-2
Protein_kinase_binding 62 Genes annotated by the GO term GO:0019901. Interacting selectively with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate. 4 0.0645 2.84 × 10-2
Biocarta_CTL_pathway 15 CTL mediated immune response against target cells 2 0.1333 3.11 × 10-2
MIPS_Emerin_complex_24 15 Emerin complex 24 2 0.1333 3.11 × 10-2
Cytoskeletal_part 235 Genes annotated by the GO term GO:0044430. Any constituent part of the cytoskeleton. 9 0.0383 3.23 × 10-2
KEGG_Cell_cycle 128 Cell cycle 6 0.0469 3.28 × 10-2
Myosin_complex 16 Genes annotated by the GO term GO:0016459. A protein complex that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments. 2 0.125 3.51 × 10-2
PID_DNAPK_pathway 16 DNA-PK pathway in nonhomologous end joining 2 0.125 3.51 × 10-2
Kinase_binding 70 Genes annotated by the GO term GO:0019900. Interacting selectively with a kinase. 4 0.0571 4.17 × 10-2
Biocarta_MCM_pathway 18 CDK Regulation of DNA Replication 2 0.1111 4.36 × 10-2
Lipoprotein_binding 18 Genes annotated by the GO term GO:0008034. 2 0.1111 4.36 × 10-2
  1. *k/K is the ratio between the number of genes in overlap (k) and the number of genes in gene set (K). This table combines the results from the collection of gene sets from canonical pathways, BioCarta, KEGG, Reactome, and GO (gene ontology) gene sets.