Table 3

Pathway information for clusters showing evidence of experiment-wide significant and suggestive linkage

Cluster

Number of genes in cluster

Pathway information using KEGG or GenMAPP^a

Pathway information using the Ingenuity software^b

67

2

Glutathione metabolism^{c, d}

Glutathione metabolism

Xenobiotic metabolism signaling Metabolism of xenobiotics by cytochrome P450

82

83

Smooth muscle contraction ^c

Circadian exercise ^c

Fatty acid synthesis^c

Valine, leucine, and isoleucine degradation^c

Blood group glycolipid biosynthesis^c

Purine metabolism

Electron transport chain

Oxidative phosphorylation

G protein signaling

Apoptosis

mRNA processing reactome

Valine, leucine, and isoleucine degradation

Oxidative phosphorylation

Purine metabolism

Xenobiotic metabolism signaling

G-protein coupled receptor signaling

cAMP-mediated signaling

PPAR signaling

B Cell receptor signaling

Blood group glycolipid biosynthesis^e

Apoptosis^e

93

48

Calcium signaling ^c

Cell cycle^c

Nucleoside G protein coupling receptor ^c

Cell cycle

Protein ubiquitination

Intergrin signaling

Actin cytoskeleton signaling

B cell receptor signaling

Leukocyte extravasation signaling

76

18

Apoptosis

Inflammatory response^c

IL-10 signaling

^aPathway information using KEGG and GenMAPP were provided in the Problem 1 data set. Pathways with more than one gene are given with the exception of the cluster 76 (inflammatory pathway).

^bPathways with more than one gene are given, except for cluster 82, which has 21 pathways with two genes. Information on pathways with ≥ 3 genes are given (with the exception of the blood group glycolipid biosynthesis and apoptosis pathways).

^cStatistically significantly associated with clusters.

^dPathways common to both approaches are given in bold font.

^eThese pathways represent two genes and have been included to show overlap between resources.

Malhotra et al. BMC Proceedings 2007 1(Suppl 1):S48