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The primary and secondary classifications of genes revealed known pathway relationships and provide the potential for discovering new pathway relationships.
The Database for Annotation, Visualization and Integrated Discovery (DAVID) [70], [71] allowed significantly enriched functional classifications of genes to be recognized.
The classifications of genes modulated after 30 min and 24 h of cobalt treatment were compared.
Our first method, classification discordance, exploits disagreement between taxonomic classifications of genes and longer assemblies.
Our results revealed several classifications of genes participating in regulation of endometrium function during early pregnancy.
We could not detect enrichment for specific functional classifications of genes in the dosage dependent or independent gene lists.
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Classification of genes by Gene Ontology (GO) groups and statistical testing of over-representation among GO groups was done separately for genes with increased and reduced expression.
Conventional algorithms used for unsupervised classifications of gene expression profiles suffer from two main limitations.
Comparison of Gene Ontology (GO) classifications of gene expression in DC3000, RL, and RL + DC3000.
Functional classifications of gene ontology (GO) terms of all unigenes are shown in Additional file 6.
The classifications of gene products in E. coli were downloaded from the GenProtEC database (Serres et al. 2004).
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