To test whether ZmbZIP genes are co-expressed in maize pathogen responses especially for their dimerization character, we calculate the Pearson correlation coefficient (PCC) among pairwise genes based on the transcriptome data from 62 microarray experiments as mentioned above (Supplementary Table S9).
Based on the transcriptome annotation, in this study, we identified most of the genes encoding enzymes involved in caffeine biosynthesis pathway.
Then based on the transcriptome, the digital gene expression analysis was conducted to examine the transcriptional response to sulfide during 6, 24 and 48 h exposure, and finally 1705, 1181 and 1494 tag-mapped genes were identified as differentially expressed genes in the 6-h, 24-h and 48-h libraries, then were further subjected to pathway analyses.
One of the aims of this study was to determine if one could select novel poxvirus vaccine vectors based on the transcriptome analysis.
Based on the transcriptome analysis in this study, we provide evidence that the conservation could possibly extend further to estrogen-induced carcinogenesis since fish is also susceptible to the carcinogens affecting humans.
The primers were designed based on the transcriptome sequences of the candidate genes (Siah et al. 2016).
Based on the transcriptome analysis, about 79.37% of the single-gene reactions and 91.93% of the multi-gene reactions were verified (Fig. 2c, d), indicating that the existence of most reactions in the model iRY1243 was reliable.
Based on the transcriptome changes, we hereby propose a putative pathway for carbon metabolism in conidia exposed to neutrophils (Fig. 8).
Based on the transcriptome-wide analysis, we did observe special patterns of cancer-specific alternative splicing.
These bins of DNA occupancies (sum -log [peak p-value]) were created for subsets of target genes, which showed differential expression (≥1.5-fold, FDR < 10%) based on the transcriptome-wide analysis of Xbra/Xbra3 double morphants at stage 32.
Recently, the publicly accessible gene expression profiles, for example, Connectivity Map (CMap) (http://www.broadinstitute.org/ccle/home), NCI-60 cell lines (http://dtp.nci.nih.gov/), LINCS (http://lincs.hms.harvard.edu/db/), and CCLE (http://www.broadinstitute.org/ccle/home), make it possible to predict drug targets based on the transcriptome data.
