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In this set of microarray data, referred to as Data Set 2, correlations between gene expression levels tend to be weaker than in Data Set 1, as well as in all other data sets we have interrogated so far [ 10].
To compare the chilling responding network of C. bungeana with Arabidopsis, the networks of chilling-regulated DEGs of Arabidopsis were constructed using previously published RNA-seq and microarray data (referred to ATH-SR and ATH-MA, respectively; see Methods for details).
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When referring to the microarray data, we refer to the normalized results for a specific probe set by the term "probe set identified transcripts," whereas we use simply "transcript" or "mRNA" when referring to the results of real-time RT-PCR analyses.
The clinical value of the PCR-GGI for tamoxifen benefit was evaluated in three independent BC populations derived from two independent institutions: 1) A series of 77 frozen ER+, node-negative and -positive adjuvant tamoxifen-only treated primary BC collected at the John Radcliff Hospital Oxfordd, UK) for which microarray data were available, referred as "OXFD".
In general, "genomics data" refers to genome-scale vector of measurements produced by various experimental assays (expression microarrays, CGH microarrays, ChIP-chip and ChIP-seq, etc).
Data refers to quantitative data required.
Catalan data refer to the Girona Cancer Registry data.
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].
We assessed the concordance between the microarray-derived GGI and the PCR-GGI measured on frozen and FFPE tissues using a series of 19 primary BC from which frozen, FFPE tissues and their corresponding microarray data were available, further referred as "IJBtest".
A small series of 19 primary BC from which frozen, FFPE tissues and their corresponding microarray data were available, further referred as "IJBtest", was used to compare the accuracy and the concordance of the microarray-derived GGI to the qRT-PCR genomic grade index (PCR-GGI).
To identify the molecular mechanism that causes cytokinesis failure in cells with trisomy 13, we referred to microarray data available for DLD1+13 cells (Upender et al., 2004).
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