Sentence examples for annotations out of from inspiring English sources
For gene ontology (GO) analysis we categorized ESTs with available RefSeq annotation (506 RefSeq annotations out of 1108 differentially expressed genes) according to GO terms for biological process, cellular component, and molecular function [see Additional file 14].
Table 2 Annotation performance using out-of-vocabulary semantic concepts.
Functional annotation was then assigned using the pathways, networks and out-of-network annotations found in VitisNet software http://www.sdstate.edu/aes/vitis/pathways.cfm[ 55, 93].
From gene annotation files from Wormbase, there were 9546 genes with tmhmm and/or SignalP annotation out of 19245 total.
37 As a result, a total of 79,275 (12.1%) constitutive exons were identified in the original mm10 annotation out of a pool of 651,678 known exons.
A fairly obvious action is to select the most specific annotation out of a set of hierarchically ordered GO terms (step 2 of the algorithm pseudocode).
For the re-annotation, out of the 23,496 probes (all control probes removed) on the bovine oligonucleotide array, only 16,620 probes that were assigned a quality score between 1 and 4 based on their specificity to hits on the bovine genome were considered.
Effective annotation and retrieval for out-of-vocabulary tags requires some method of relating the semantic similarity of tags, for example, the WordNet similarity metric used in this work.
As with annotation, text-based retrieval with out-of-vocabulary concepts is significantly more difficult than with in vocabulary concepts, but including the concept-concept links based on the measure of WordNet similarity helps to ameliorate retrieval performance.
This annotation collection table (Additional file 1) covered 130 GO annotations extracted out of a total of 4189 annotations (about 3%).
Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database as our source of annotations, 583 out of 803 Populus genes annotated as being involved in hormone biosynthesis [ 52] were detected in the four libraries and 59 of these genes were differentially expressed in either P. euphratica or P. pruinosa under salt stress (Additional file 3).
