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Table 2 Pathways associated with the selected genes in SJCRH data

From: Improving the Performance of SVM-RFE to Select Genes in Microarray Data

Pathway

RFE

RFE- Annealing

SQRT-RFE

Apoptosis

2

2

2

Apoptosis_GenMAPP

3

3

3

Apoptosis_KEGG

2

2

2

Arginine and proline metabolism

2

2

2

Biosynthesis of steroids

1

1

1

Calcium signaling pathway

19

18

17

Calcium_regulation_in_cardiac_cells

6

4

4

Cell_cycle_KEGG

8

8

9

Cholesterol_Biosynthesis

1

1

1

Circadian_Exercise

2

2

2

DNA_replication_Reactome

0

0

1

Electron_Transport_Chain

1

1

1

Fructose and mannose metabolism

1

1

1

Gl_to_S_cell_cycle_Reactome

6

6

7

G_Protein_Signaling

6

4

4

Galactose metabolism

1

1

1

Glutathione metabolism

1

1

1

Glycerolipid metabolism

1

1

1

Glycerophospholipid metabolism

3

3

3

Glycine, serine and threonine metabolism

2

2

2

Glycolysis/Gluconeogenesis

1

1

1

Glycolysis_and_Gluconeogenesis

1

1

1

GPCRDB_Class_A_Rhodopsin-like

0

1

0

Hypertrophy _model

1

1

1

Inflammatory_Response_Pathway

1

1

4

Inositol phosphate metabolism

4

4

0

Integrin-mediated_cell_adhesion_KEGG

4

4

4

MAPK_Cascade

1

1

1

mRNA_processing_Reactome

2

2

3

Nicotinate and nicotinamide metabolism

1

1

1

Ovarian_Infertility_Genes

3

3

3

Oxidative phosphorylation

1

1

1

Pentose phosphate pathway

1

1

1

Phosphatidylinositol signaling system

4

4

3

Prostaglandin_synthesis_regulation

1

0

1

Proteasome_Degradation

1

1

1

Purine metabolism

3

2

2

Pyrimidine metabolism

2

2

2

Smooth_muscle_contraction

12

10

10

Statin_Pathway_PharmGKB

0

0

1

TGF_Beta_Signaling_Pathway

4

4

4

Terpenoid biosynthesis

1

1

1

Type I diabetes mellitus

4

5

5

Ubiquitin mediated proteolysis

2

2

2

Urea cycle and metabolism of amino groups

2

2

2

Wnt_signaling

3

3

2

  1. This table lists the various known pathway associations with the size 200 gene sets selected by the algorithms using the SJCRH data. The values in the table represent the number of genes associated with that pathway in each of the sets. In general there was considerable overlap in the genes selected (over 90%). The pathways with the least consistency are shown in boldface. Pathway data was derived using NetAffx [13].
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BMC Bioinformatics

ISSN: 1471-2105

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