Database of mRNA gene expression profiles of multiple human organs.
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 approximately 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.
Son
Chang Gue
CG
Advanced Technology Center, Oncogenomics Section, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Gaithersburg, Maryland 20877, USA.
Bilke
Sven
S
Davis
Sean
S
Greer
Braden T
BT
Wei
Jun S
JS
Whiteford
Craig C
CC
Chen
Qing-Rong
QR
Cenacchi
Nicola
N
Khan
Javed
J
D016000:Cluster Analysis; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000235:genetics*
D012333:RNA, Messenger
Mol Biol Cell. 2004 Feb;15(2):649-56
14657249
Nat Genet. 2003 Apr;33(4):459-61
12640453
Cold Spring Harb Protoc. 2020 Jan 2;2020(1):101659
31896611
Oncogene. 2005 Feb 24;24(9):1533-41
15592497
Am J Med Genet. 2001 May 8;105(4):317-20
11378843
Cytogenet Cell Genet. 1982;33(3):204-12
6889950
Cancer. 2002 May 15;94(10):2552-60
12173320
Cancer Res. 2003 Nov 1;63(21):7158-66
14612509
J Neurosci. 2002 Jan 1;22(1):218-25
11756505
Science. 2003 Oct 10;302(5643):249-55
12934013
Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4465-70
11904358
Am J Hum Genet. 2004 Apr;74(4):761-4
15024693
Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7
15075390
Biotechniques. 2000 Sep;29(3):548-50, 552-4, 556  passim
10997270
J Pathol. 2004 Jul;203(3):789-97
15221938
Nat Genet. 2000 May;25(1):25-9
10802651
Cytogenet Genome Res. 2003;103(1-2):58-62
15004465
Nucleic Acids Res. 2002 Jan 1;30(1):214-7
11752297
J Mol Diagn. 2002 Feb;4(1):30-6
11826185
J Biomed Opt. 1997 Oct;2(4):364-74
23014960
J Biotechnol. 2004 Sep 9;112(3):225-45
15313001
Nat Rev Cancer. 2003 Mar;3(3):203-16
12612655
Science. 2001 Feb 16;291(5507):1304-51
11181995
EMBO J. 1997 Jun 2;16(11):2985-95
9214616
C R Biol. 2003 Oct-Nov;326(10-11):1067-72
14744114
Genome Res. 2004 Apr;14(4):742-9
15060018
Nature. 2001 Feb 15;409(6822):860-921
11237011