After the annotation merging by cuffmerge, 157,229 genes were annotated, within which, 101,040 genes have been annotated with the publishing of the reference genome.
Genes were annotated on all of the potato BACs using a semi-automated annotation pipeline; a total of 287 genes were annotated within the 18 potato BACs.
Using the same annotation pipeline, 221 genes (139 known/putative, 17 expressed, and 65 hypothetical genes) were annotated within the tomato BACs/contigs.
Another represented protein family encoded by DEGs that are annotated within chromatin-related GO categories was the histone protein family.
f Six putative genes were annotated within the 28.5 kb region according to MSU Rice Genome Annotation Release 6.1.
Globally, the most represented protein family encoded by DEGs annotated within chromatin-related GO categories was the helicase protein superfamily.
We also added all false-positive terms, i.e., terms indexed by our system but not annotated within the corpus (e.g., "peptide" and "carcinogen"), to our stop-word list, which further improved performance.
A functional classification of the genes annotated within the integration clusters was carried out by the Ingenuity® software.
Results indicate 3,898 contigs were annotated with 2781 InterPro (IPR) items, while 5,411 contigs were annotated within 132 KEGG pathways.
A similar approach using the published genetic and proteomic interactions annotated within the SGD identified five DOX resistance genes that were not detected in the primary screen and exhibited an intermediate sensitivity to DOX induced cytotoxicity (Fig. 4).
The enrichment analysis computes the probability that a set of genes that are annotated within a specific category would occur by chance and the results are given in the form of p-values.
