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Addendum: A Web site supported by the gas industry has posted a long, annotated response to the film.
Among the 21 patients with evaluable tissue and annotated response, 9 had a PathCR (47.3%).
For response regulators the differences between identified domains and annotated response regulators are even larger, indicating more divergence.
This cohort is composed of 226 pre-treatment samples with annotated response data (pCR vs. RD) after neoadjuvant anthracycline/taxane-based chemotherapy (without trastuzumab for HER2+ disease).
To compare chemotherapy response data, we used the clinical data of one of the datasets (MAQC2 [GSE20194] [ 21]) evaluated by Haibe-Kains et al. [ 6], which is composed of 230 pre-treatment samples with annotated response data (pCR vs. residual disease [RD]) after neoadjuvant anthracycline/taxane-based chemotherapy.
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To determine the expression patterns of the two genes annotated as "response to cold" in response to cold stress, a qRT-PCR was performed using the total RNA of the two parents DN422 and KY131 subjected to cold water conditions.
Based on GO term assignment and KEGG annotation, 187 assembled unigenes were annotated in "response to stress" under the level 3 classification for "biological process", while 96 assembled unigenes were associated with the pathways of "xenobiotics biodegradation and metabolism" under the KEGG metabolism pathway.
Not surprisingly, most of these TFs are annotated with response to different stimulus in Arabidopsis, such as response to chitin and external stress, given that the microarray data we used were measured in response of Arabidopsis exposed to different abiotic stresses.
However, not all of these genes are directly regulated by GlnR, since the set includes 7 genes themselves annotated as response regulators, making the genes under the control of these other response regulators only indirectly controlled by GlnR.
Two genes, LOC_Os06g39740 and LOC_Os06g39750, were annotated as "response to cold" by gene ontology (GO) analysis.
According to the results of the gene ontology (GO) analysis, LOC_Os06g39740 and LOC_Os06g39750 were annotated as "response to cold".
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