Abstract
BackgroundCategorizing protein-encoding transcriptomes of normal tissues into housekeeping genes and tissue-selective genes is a fundamental step toward studies of genetic functions and genetic associations to tissue-specific diseases. Previous studies have been mainly based on a few data sets with limited samples in each tissue, which restrained the representativeness of their identified genes, and resulted in low consensus among them.ResultsThis study compiled 1,431 samples in 43 normal human tissues from 104 microarray data sets. We developed a new method to improve gene expression assessment, and showed that more than ten samples are needed to robustly identify the protein-encoding transcriptome of a tissue. We identified 2,064 housekeeping genes and 2,293 tissue-selective genes, and analyzed gene lists by functional enrichment analysis. The housekeeping genes are mainly involved in fundamental cellular functions, and the tissue-selective genes are strikingly related to functions and diseases corresponding to tissue-origin. We also compared agreements and related functions among our housekeeping genes and those of previous studies, and pointed out some reasons for the low consensuses.ConclusionsThe results indicate that sufficient samples have improved the identification of protein-encoding transcriptome of a tissue. Comprehensive meta-analysis has proved the high quality of our identified HK and TS genes. These results could offer a useful resource for future research on functional and genomic features of HK and TS genes.
Highlights
In the last decade, massive gene expression microarray data has opened an avenue toward transcriptomic study
Some previous studies identified constantly expressed genes among normal and disease tissues as HK genes or reference genes [5,6,7], in this study, we focused on the identification of HK genes which are universally expressed in all normal tissues [2]
To define the PE transcriptome of each tissue, we developed the fraction Present weighted expression intensity (FPEI), which overall performs better than expression intensity and fraction Present [26] in gene expression assessment
Summary
Massive gene expression microarray data has opened an avenue toward transcriptomic study. Benefitting from this progress, the ideas of housekeeping (HK) genes and tissueselective (TS) genes can be investigated on a large-scale manner. Previous microarray-based studies endeavored to collect diverse tissues [3,8,9,10,11,12,13], but lack of sample availability for each tissue (less than three samples for a tissue in average) has limited the representativeness of the data. Categorizing protein-encoding transcriptomes of normal tissues into housekeeping genes and tissue-selective genes is a fundamental step toward studies of genetic functions and genetic associations to tissue-specific diseases. Previous studies have been mainly based on a few data sets with limited samples in each tissue, which restrained the representativeness of their identified genes, and resulted in low consensus among them
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