Abstract
Housekeeping (HK) genes are constitutively expressed genes that are required for the maintenance of basic cellular functions. Despite their importance in the calibration of gene expression, as well as the understanding of many genomic and evolutionary features, important discrepancies have been observed in studies that previously identified these genes. Here, we present Housekeeping and Reference Transcript Atlas (HRT Atlas v1.0, www.housekeeping.unicamp.br) a web-based database which addresses some of the previously observed limitations in the identification of these genes, and offers a more accurate database of human and mouse HK genes and transcripts. The database was generated by mining massive human and mouse RNA-seq data sets, including 11 281 and 507 high-quality RNA-seq samples from 52 human non-disease tissues/cells and 14 healthy tissues/cells of C57BL/6 wild type mouse, respectively. User can visualize the expression and download lists of 2158 human HK transcripts from 2176 HK genes and 3024 mouse HK transcripts from 3277 mouse HK genes. HRT Atlas also offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments. Specific primers and predicted modifiers of gene expression for some of these HK transcripts are also proposed. HRT Atlas has also been integrated with a regulatory elements resource from Epiregio server.
Highlights
Housekeeping (HK) genes have been classically defined as genes that are required for the maintenance of basic cellular functions, important for the existence of any cell type
HK genes are useful as references of gene expression in molecular biology and computational experiments [3,4,5,6,7,8,9], as well as in our understanding of various structural and functional genomics and evolutionary features [10,11,12,13]
The importance of the precise identification of HK genes stems from the fact that these genes are used as internal controls for the calibration of quantitative PCR, a workhorse technique in molecular biology and biotechnology laboratories used to quantitatively estimate the expression of any gene of interest under different experimental conditions [9, 14]
Summary
Housekeeping (HK) genes have been classically defined as genes that are required for the maintenance of basic cellular functions, important for the existence of any cell type. HRT Atlas offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments.
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