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.
Data for annotation and functional classification of genes was obtained through Genespring (Agilent), the Gene Ontology Consortium [85], Aceview (www.aceview.org) [86], and previous studies.
Figure 1 Classification of genes regulating yield-traits.
Classification of genes was done using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (http://www.genome.jp/kegg/).jp/kegg/
Correct classification of genes into gene families is important for understanding gene function and evolution.
The standard vaccinia classification of genes as early, intermediate, or late is based on temporality of transcription initiation.
The functional classification of genes showing reduced expression in the lymphomas was frequently related to T-cell immunity (Figure 3A, Table S2).
The classification of genes into dynamic or kinetic was checked with the Pharmacogenomics Knowledge database (PharmGKB; http://www.pharmgkb.org accessed 2009 November 10, archived URL http://www.webcitation.org/5lBChBcLk).org/5lBChBcLk
This kind of analysis permits the classification of genes according to the whole transcriptional response because it captures the changes in both mRNA synthesis (TR) and mRNA degradation.
Similar statistical analysis was done for functional classification of genes in islands, where the number of genes in each VFDB category was used in the calculation.
Functional classification of genes differentially expressed by non-mobilized versus mobHSC revealed that ∼half of these encode unknown genes or uncharacterized EST sequences.
