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The "endomembrane system" cellular compartment category was consistently enriched in genes with significantly altered expression.
Finally, within the "Cellular compartment" category, the "Membrane", "Integral to membrane" and "Cytoplasm" GO terms constituted the most overrepresented category for the genes with increased transcript accumulation in ripe fruit at 217 DPA.
Due to mapping biases between human and chimpanzee ribosomal proteins and pseudogenes, we removed all genes associated with the Gene Ontology Cellular Compartment category 'ribosome' (GO 0005840, n = 141) and all annotated pseudogenes in Ensembl release 65 (n = 3170, December 2011, the oldest available archival version of Ensembl) from the data at this point.
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No strong correlations were observed for GO biological process and cellular compartment categories (data not shown).
The 110 unique DE genes that possess functional annotation are listed in Table S1 within broad functional and cell compartment categories.
Table 3 and Dataset S4 provide GO (Drosophila melanogaster slim) protein annotations under Biological Process, Molecular Function and Cellular Compartment categories for the most significantly enriched annotation observed in each population.
In the cellular compartments category, 'cell part' (29%) was the most represented term, followed by 'membrane-bounded organelle' (20%) and 'organelle part' (16%) (data not shown).
In the molecular function category, "binding" (41.8%) was the most dominant term, followed by "catalytic activity" (36.6%); in the cellular compartments category, "cell part" (42.91%) was the most represented term, followed by "membrane-bounded organelle" (29.34%) and "organelle part" (10.04%).
Regarding the cellular compartment GO category, the extracellular matrix (ECM) part was highly enriched in the list of DE genes.
A number of enzymes in particular compartments are category II; their concentrations in those compartments can be from zero to very high without any consequence on the glycan flux profile.
GO-terms in the Biological Process (BP), Molecular Function (MF) and Cellular Compartment (CC) categories that were significantly enriched (p-value < 10E-7) theards top tof of the lists of transcripts ranked according to correlation to each of the quantified metabolites.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com