A compendium of gene expression in normal human tissues

Abstract

This study creates a compendium of gene expression in normal human tissues suitable as a reference for defining basic organ systems biology. Using oligonucleotide microarrays, we analyze 59 samples representing 19 distinct tissue types. Of ∼7,000 genes analyzed, 451 genes are expressed in all tissue types and designated as housekeeping genes. These genes display significant variation in expression levels among tissues and are sufficient for discerning tissue-specific expression signatures, indicative of fundamental differences in biochemical processes. In addition, subsets of tissue-selective genes are identified that define key biological processes characterizing each organ. This compendium highlights similarities and differences among organ systems and different individuals and also provides a publicly available resource (Human Gene Expression Index, the HuGE Index, http://www.hugeindex.org ) for future studies of pathophysiology.

Repetitive sequence environment distinguishes housekeeping genes

“…We assembled a list of tissue-specific genes by combining the published lists of two studies (Warrington et al, 2000;Hsiao et al, 2001). Genes from all lists were identified by either Genbank RefSeq ID or Unigene ID and were converted to RefSeq ID via DAVID Tools (http://apps1.niaid.nih.gov/david) (Dennis et al, 2003).…”

“…We chose for our analysis 1000 randomly selected autosomal Reference sequence (RefSeq) genes, published lists of 583 housekeeping genes (Eisenberg and Levanon, 2003), and 468 tissue-specific genes (Warrington et al, 2000;Hsiao et al, 2001). For each gene, we initially considered a region extending 100-kb upstream from the transcription start and 100-kb downstream from the transcription end, but excluding the transcribed gene region.…”

Human housekeeping genes are compact

“…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.…”