GO-annotated consensus sequences belonged to the biological process, cellular component, and molecular function clusters and distributed among more than 50 categories, including biochemistry, metabolism, growth, development, apoptosis, and immune defence.
High variance genes (53 total) were enriched in four molecular function clusters associated with (1) monooxygenase or other heme binding activity (Cyp2b2, Cyp2d26, Cyp2d9, Cyp2d10, Cyp4b1, Cyp7a1, Cyp8b1, Cyp17a1, Hbb), (2) cytokine, growth factor, or other receptor binding activity, (3) carbohydrate binding (Apcs, Lpl, TSP-2), and (4) transporter activity.
In the "Molecular function" cluster, the category "Receptor binding or activity" displayed most changes, where most transcripts were downregulated.
The major subcategories were as follows: three subcategories ('cell'cellell part' and 'organelle') in the cellular component cluster; two subcategories ('binding' and 'catalytic activity') in the molecular function cluster; and three subcategories ('cellular process', 'metabolic process' and 'response to stimulus') in the biological process cluster.
GO-annotated unigenes belonged to the biological processes, cellular components, and molecular functions clusters and were distributed across more than 40 categories, including biochemistry, metabolism, growth, development, and apoptosis.
In the molecular function, the clusters relating to "binding" and "catalytic activity" were enriched (21,089 and 12,443, respectively).
In the molecular function category, clusters 1 and 4 contained approximately two-fold more genes related to 'transporter activity' (11.6% and 14.5% respectively) than cluster 2 (5.3%), and cluster 2 contained approximately four-fold more genes in the 'protein binding' (13.9%) category than cluster 4 (3.3%).
Functional categories (biological process and molecular function) were clustered with the K-Means method using 1,000 iterations.
Figure 1A shows GO functional groups for known transcripts represented on the AH006 array and a detailed description of the GO molecular function (MF) cluster is displayed in Figure 1B which indicates uniform distribution of probes with binding and catalytic functions.
Based on Gene Ontology function classification, 824 clusters (3144 ESTs) are assigned into the organizing principle of molecular function and 1719 clusters (5472 ESTs) of biological process.
The full KEGG pathway analysis and the enriched GO categories Biological Process, Cellular Component and Molecular Function for each cluster are listed in Additional file 2. Cluster 1 was strongly associated with an extracellular matrix theme in the enriched KEGG pathway and GO Cellular Component (CC) analyses.
