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

Abstract

Gene expression levels of about 7,000 genes were measured in 11 different human adult and fetal tissues using high-density oligonucleotide arrays to identify genes involved in cellular maintenance. The tissues share a set of 535 transcripts that are turned on early in fetal development and stay on throughout adulthood. Because our goal was to identify genes that are involved in maintaining cellular function in normal individuals, we minimized the effect of individual variation by screening mRNA pooled from many individuals. This information is useful for establishing average expression levels in normal individuals. Additionally, we identified transcripts uniquely expressed in each of the 11 tissues.

Human housekeeping genes are compact

“…We used the genomic structure to test the remaining genes, and found a statistically significant difference between them and our HK gene set. The differences between our results and those of earlier studies [3,4] could be due to the fact that the database we used was based on more advanced chip technology and included many more different tissues, giving it more discriminative power to identify HK genes.…”

“…These genes are called housekeeping genes (HK genes) [1]. HK genes can be used to calibrate measurements of gene expression [2].They might also help to define the minimal gene complement needed for a human cell [1].Several attempts have been made recently to define the complete set of HK genes [3,4].Microarrays are often used to identify sets of genes that are expressed either ubiquitously or in specific tissues or conditions. However, the technique is technically demanding and prone to artifacts, so independent evidence is often required to confirm the results.…”

“…However, the technique is technically demanding and prone to artifacts, so independent evidence is often required to confirm the results. In principle, identifying the set of HK genes using microarray data is straightforward; one need only look for genes that are expressed in all tissues and all experimental conditions.Employing such an approach has so far resulted in two lists of HK genes [3,4]. However, problems in probe design, measurement noise and other artifacts introduce inevitable errors in such lists.…”

“…Employing such an approach has so far resulted in two lists of HK genes [3,4]. However, problems in probe design, measurement noise and other artifacts introduce inevitable errors in such lists.…”

Microarray profiling of skeletal muscle tissues from equally obese, non-diabetic insulin-sensitive and insulin-resistant Pima Indians

“…The hybridization mixture was heated to 99°C for 5 min and equilibrated at 45°C for 5 min before hybridization in the oligonucleotide array chamber at 45°C for 16 to 17 h. Each hybridization sample was hybridized to the Affymetrix GeneChip Hu6800 Array (Santa Clara, Calif., USA) and Human 35 K set consisting of about 5600 unambiguous full-length cDNAs (after masking for the ambiguous probe set designs using the class AB mask as per the manufacturer's instruction that filtered out probe sets containing less than 10 unambiguous probe pairs in the Hu6800 array) and about 35,000 clustered human EST transcripts, respectively. After hybridization, the solution was removed and the probe arrays were washed and stained using the GeneChip Fluidics station protocol EukGE-WS2, as described previously [18]. The protocol consisted of non-stringent and stringent washes after hybridization, followed by a staining procedure using streptavidin-phycoerythrin solution (SAPE), and a post-stain wash. Signal amplification was achieved using antibody against streptavidin, after a final wash.…”