A novel approach for human whole transcriptome analysis based on absolute gene expression of microarray data

Background. Although the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under the specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays. Given that the Y chromosome is absent in female subjects, we used it as a new approach for absolute gene expression analysis in which the fluorescence of the Y chromosome genes of female subjects was used as the background fluorescence for all the probes in the microarray. This fluorescence was used to establish an absolute gene expression threshold, allowing the differentiation between expressed and non-expressed genes in microarrays.

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Bikel S, Jacobo-Albavera L, Sánchez-Muñoz F, Cornejo-Granados F, Canizales-Quinteros S, Soberón X, Sotelo-Mundo RR, Del Río-Navarro BE, Mendoza-Vargas A, Sánchez F, Ochoa-Leyva A