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CWR performed statistical analysis of microarray data, completed the Ingenuity Pathway Analysis (IPA) and qRT-PCR analyses, and wrote the first draft of the manuscript.
AMH carried out analysis of cell line microarray data, completed in vitro studies including cell migration, invasion and drug sensitivity assays, as well as gene knockdown experiments, and drafted the manuscript.
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There are overwhelming data available for the yeast genome, including many public microarray data, complete promoter sequences, whole-genome transcription factor binding (ChIP-chip) data, protein-protein interactions, just to name a few.
Quality assurance of microarray data was completed using the affyQAReport function from the Bioconductor package affyQCReport.
Network analysis of the microarray data was completed using the Ingenuity Pathway Analysis software [ 50].
However, most of the downstream analyses for microarray data require complete datasets.
To further validate our microarray data, regression analysis was completed for the two data sets.
The microarray data included 56 complete trios from the HapMap [30] cell line panels originating from the Yoruba in Ibadan, Nigeria (YRI) and from Utah residents with ancestry from northern and western Europe (CEU).
This function will automatically list all available microarray data and download complete microarray content directly into the user's MATLAB workspace.
The latter cohort consisted of all evaluable breast cancers from published microarray data that had complete pathological and clinical outcome data.
The results support the microarray data, demonstrating almost complete lack of Snca expression in the Cln1/5 dko cortex (supplementary material Fig. S7A).
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