Exploration of non-hierarchical classification methods combined with linkage analysis to identify loci influencing clusters of co-regulated transcripts

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.

ISSN: 1753-6561