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The upregulated genes mainly belonged to three different functional categories: nitrogen metabolism-related genes, including a set of nitrogen fixation-related genes; a large number of genes encoding transporter and membrane proteins; and genes with unknown function.
One interesting common trait in all the comparisons made of the transcriptional changes observed either by temperature or strains was the presence of functional categories "nitrogen, sulfur and selenium metabolism", "sulfur metabolism" and "metabolism of methionine" in the genes up-regulated at low temperature (Table 2).
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The category nitrogen was used to look for a pattern of associating nitrogen-fixing processes with peanut plants.
Thus it is more suitable to add these genes into the category nitrogen, sulfur and selenium metabolism.
If all the categories involving nitrogen are grouped, horizontal gene transfers of genes involved in nitrogen acquisition and metabolism are in fact the most populous category.
BPs are classified into 2 categories - Nitrogen containing BPs (pamidronate, alendronate, risedronate, zoledronate, etc).
Genes extremely expressed in moderate copper for SK1, constitutively meagerly expressed in S288C, and variably expressed in other strains grouped into a cluster of 102 genes enriched for GO categories including nitrogen compound transport, amino acid catabolism, and thiamine metabolism.
Based on their structure BPs can be divided into two categories, non-nitrogen-containing bisphosphonates (non N-BPs) and nitrogen-containing bisphosphonates (N-BPs).
The KEGG pathways for phenylalanine metabolism (map00360), methionine metabolism (map00271), and arginine and proline metabolism (map00330) can be grouped into a category of nitrogen metabolism.
Eleven nutrients belonging to two categories viz.; nitrogen sources and salt sources along with three physical parameters and a buffer were screened.
Analysis revealed that differentially expressed genes in functional categories related to nitrogen metabolism show a trend of significant down-regulation in GS poplars compared to the WT, including genes encoding nitrate and nitrite reductases.
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