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Some of the most highly co-evolved interactions are between plants and biotrophic pathogens.
Table S1 shows the 300 most highly co-expressed Arabidopsis genes obtained for each of the three baits, IRX9, IRX14, and IRX10.
FRA8 produced a tight network with an MR<192.8 for the 300th most highly co-expressed genes (Table 1), but this network did not overlap considerably with the network defined by xylan backbone synthesis genes IRX9, IRX10 and IRX14.
The four additional GT groups identified were RGP (GT75) and GT61 in rice, PGSIP1 and PGSIP3 in Arabidopsis, and GT31 proteins in both species but most highly co-expressed in rice.
Almost all the components identified in the previous studies are also included in the most highly co-expressed genes in our study (i.e. the 124 Arabidopsis genes in Table S2 include 83% of the genes published in any of the four references. The entire Arabidopsis co-expression list in Table S1 includes 93% of the genes published in any of the four references).
To select the best rice candidate genes for co-expression analysis we identified the IRX9, IRX10 and IRX14 homologs that fulfilled the following criteria: 1) 'mountain-type' expression profile (Figure 2B), 2) lowest maximum MR in the 300 most highly co-expressed genes and 3) maximum number of shared genes.
Additional file 10: List of the top two hundred genes most highly co-expressed with AT4G28720 and AT5G51470.
Next we generated lists of genes that are most highly co-expressed with IL-8 in these two virtual tissues.
A first glance at the most highly co-enriched probed regions revealed a preponderance of telomeres and noncoding RNAs (ncRNAs) (Table 1).
An expression correlation analysis was performed to identify genes in the Arabidopsis genome that are most highly co-expressed with PSY.
Most strikingly, NH3 was most highly co-expressed with RH1, showing 24 positive correlations and no inverse correlations out of the 32 data sets analyzed.
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