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This analysis includes 21,460 genes for which there are both microarray data and assigned duplication status.
Core genome size was calculated using both microarray data and OrthoMCL output and pan-genome size was calculated using OrthoMCL output alone.
For example, where both microarray data and qRT-PCR data showed that there was a large up-regulation of RNAIII after challenge or growth exposure in MRSA252, pronounced down-regulation was observed in SH1000 by qRT-PCR.
This gene also uniquely expressed in trichomes according to both microarray data and RT-PCR amplification.
Similar upregulation and downregulation trends were seen with both microarray data and QRT-PCR data for all 13 genes.
NCA has shown its effectiveness in discovering regulators and inferring TFAs when both microarray data and transcription factor-gene connectivity information are available.
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We used both the microarray data and normalised RNA-Seq expression values to test for the presence of contiguous gene combinations (i.e. windows of genes located next to each other within the genome) that were predictive of sex.
Both the microarray data and design are available at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GSE48360; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GSE48361; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi acc=GSE55931.nih.gov/geo/query/acc.cgi acc=GSE55931
We compared genes that are found in both the microarray data and the SAGE data based on their fold increase.
Oncomine is a web-based database system that focuses on cancer related genomics data and includes both raw microarray data and gene sets (referred to as "molecular concepts") [ 9].
In fact, most of the correlation coefficients themselves are highly similar to those presented in Table 1, indicating that both the microarray data and RPKM data exhibit similar relations to the gene expression levels.
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