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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.