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As shown in Figure 2, mini-proteins are involved in broad functional classes, including information storage and processing, cellular processes and signalling, and metabolism.
Divisions into broad functional classes are shown in Figure 4.
Peripheral blood monocytes, on the other hand, can be subdivided into two broad functional classes.
However, Additional file 2 provides an overview of the broad functional classes that are represented by the genes on the array.
Annot8r assigns GO terms to unigenes based on BLASTX similarity (E-value < 10-5) to proteins with known GO annotations; results are summarized via GO-slim terms corresponding to broad functional classes.
Specifically, our primary analysis uses a subset of Gene Ontology (GO) biological process terms that correspond to broad functional classes ("Informative Terms" [ 25], see Materials and Methods for more details).
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Next, we consider another set consisting of broader functional classes corresponding to "Informative Terms," which are computed according to the method presented in Huang et al. [ 25].
Here the objectives were to analyze the CAZyme domain families within each broader functional class present in each genome to determine whether the presence of unique domain families contributed to the organismal complexity of vascular and/or seed producing plants.
Together, these studies identified approximately 48 selection-candidate genes belonging to a broad range of functional classes as well as some genes of unknown function.
Interestingly, while the genes detected show a broad distribution of functional classes, we detected a statistically significant enrichment for genes whose functions are associated with spermatogenesis (P = 0.002, Fisher's exact test).
The genes that were differentially expressed in EGFR-mutant NSCLC cell lines fell into a broad range of functional classes (categorized in the Gene Ontology Molecular Functions, www.geneontology.org) (Files S3 and S4).
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