Human housekeeping genes are compact

doi:10.1016/S0168-9525(03)00140-9

Trends in Genetics

Volume 19, Issue 7, July 2003, Pages 362-365

https://doi.org/10.1016/S0168-9525(03)00140-9 Get rights and content

Abstract

We identify a set of 575 human genes that are expressed in all conditions tested in a publicly available database of microarray results. Based on this common occurrence, the set is expected to be rich in ‘housekeeping’ genes, showing constitutive expression in all tissues. We compare selected aspects of their genomic structure with a set of background genes. We find that the introns, untranslated regions and coding sequences of the housekeeping genes are shorter, indicating a selection for compactness in these genes.

Section snippets

Assignment of housekeeping genes

A recently published database provides microarray expression data for Affymetrix U95A chip, containing 12 600 probes, and hybridized to 101 different samples [9] from 47 different human tissues and cell lines. These samples are mainly from the normal human physiological state, and therefore this dataset provides a description of the normal mammalian transcriptome.

We calculated the distribution of the number of different tissues in which a gene is expressed. Discarding probes for which the

Length analysis of HK genes

Table 1 compares the lengths of various parts of the HK genes and the background genes. The alignment data was taken from the UCSC genome browser (http://genome.ucsc.edu) [16]. We excluded 322 genes that do not have a unique alignment, as well as 1242 genes that were not expressed in any tissue (to avoid potential problems because of defective probes). This left 532 HK genes and 5404 non-HK genes. The histograms in Fig. 1b–d compare HK genes with the other genes by total intron length, 5′ UTR

Acknowledgements

We thank Andrew Su for helpful discussion and for providing us with the RefSeq mapping. Gady Cojocaru and Rotem Sorek are acknowledged for comments on the manuscript and insightful discussion.

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Trends in Genetics

Genome analysisHuman housekeeping genes are compact

Abstract

Section snippets

Assignment of housekeeping genes

Length analysis of HK genes

Acknowledgements

J. Biol. Chem.

J. Biol. Chem.

Trends Genet.

Anal. Biochem.

Curr. Opin. Genet. Dev.

Further defining housekeeping, or ‘maintenance,’ genes focus on ‘a compendium of gene expression in normal human tissues’

Physiol. Genomics

A novel method for real time quantitative RT–PCR

Genome Res.

Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes

Physiol. Genomics

A compendium of gene expression in normal human tissues

Physiol. Genomics

Principles of biochemistry

Biochemistry

Genome analysis
Human housekeeping genes are compact