Database of mRNA gene expression profiles of multiple human organs

Abstract

Genome-wide expression profiling of normal tissue may facilitate our understanding of the etiology of diseased organs and augment the development of new targeted therapeutics. Here, we have developed a high-density gene expression database of 18,927 unique genes for 158 normal human samples from 19 different organs of 30 different individuals using DNA microarrays. We report four main findings. First, despite very diverse sample parameters (e.g., age, ethnicity, sex, and postmortem interval), the expression profiles belonging to the same organs cluster together, demonstrating internal stability of the database. Second, the gene expression profiles reflect major organ-specific functions on the molecular level, indicating consistency of our database with known biology. Third, we demonstrate that any small (i.e., n ∼ 100), randomly selected subset of genes can approximately reproduce the hierarchical clustering of the full data set, suggesting that the observed differential expression of >90% of the probed genes is of biological origin. Fourth, we demonstrate a potential application of this database to cancer research by identifying 19 tumor-specific genes in neuroblastoma. The selected genes are relatively underexpressed in all of the organs examined and belong to therapeutically relevant pathways, making them potential novel diagnostic markers and targets for therapy. We expect this database will be of utility for developing rationally designed molecularly targeted therapeutics in diseases such as cancer, as well as for exploring the functions of genes.[Supplemental material is available online at

Credentialing Preclinical Pediatric Xenograft Models Using Gene Expression and Tissue Microarray Analysis

“…The web interface offers a broad variety of options for data query, normalization, and visualization. It also offers an option to compare the expression profiles to our expression database of normal human tissues (25).…”

Diagnosis of the Small Round Blue Cell Tumors Using Multiplex Polymerase Chain Reaction

“…4 A subset of these genes (n ϭ 34), which are specific to each diagnostic category, were selected for multiplex RT-PCR as seen in Table 2. In addition, several genes (n ϭ 5) differentially expressed in NB tumors and normal tissues from Son et al 7 and an unpublished result were also included in the assay (Table 2).…”

Identification of new genes associated with breast cancer progression by gene expression analysis of predefined sets of neoplastic tissues

“…It has been recently demonstrated that the expression profile of any randomly selected set of genes with a sufficient width (around 100) can correctly identify the kind of human tissue or organ from which the RNA was extracted. 14 Another unexpected conclusion is that these prognostic signatures very rarely include known progression-associated genes or clearly point to novel pathways or molecules associated with cancer progression. Therefore their exceptional prognostic and predictive value does not parallel an equal power to identify new potential targets for therapy and drug development.…”