title: Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  This 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan.
authors.forename: Cheng-Wei
authors.initials: CW
authors.lastname: Chang
authors.forename: Wei-Chung
authors.initials: WC
authors.lastname: Cheng
authors.forename: Chaang-Ray
authors.initials: CR
authors.lastname: Chen
authors.forename: Wun-Yi
authors.initials: WY
authors.lastname: Shu
authors.forename: Min-Lung
authors.initials: ML
authors.lastname: Tsai
authors.forename: Ching-Lung
authors.initials: CL
authors.lastname: Huang
authors.forename: Ian C
authors.initials: IC
authors.lastname: Hsu
mesh_terms: D001921:Brain / Q000378:metabolism; D005786:Gene Expression Regulation; D020043:Genes, Essential / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016366:Open Reading Frames / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics*; D018401:Sample Size; D059467:Transcriptome