TY - JOUR
T1 - Comparing genomic expression patterns across species identifies shared transcriptional profile in aging
AU - McCarroll, Steven A.
AU - Murphy, Coleen T.
AU - Zou, Sige
AU - Pletcher, Scott D.
AU - Chin, Chen Shan
AU - Jan, Yuh Nung
AU - Kenyon, Cynthia
AU - Bargmann, Cornelia I.
AU - Li, Hao
N1 - Funding Information:
We thank A. Malmberg, C. Patil, J. DeRisi and I. Herskowitz for discussions and comments on the manuscript; A. Dillin and J. Lehrer-Graiwer for assistance in building the C. elegans microarrays; S. Meadows for assistance with D. melanogaster expression profiling; and J. DeRisi and H. Bennett for advice, instruction and use of their equipment. This work was supported by a grant from the US National Institute on Deafness and Other Communication Disorders to C.I.B., a grant from the Ellison Foundation to C.K., and a Sandler Grant, Packard Fellowship and Life Sciences Informatics grant to H.L. S.A.M. was a Howard Hughes Medical Institute graduate research fellow; C.T.M. is a Life Sciences Research postdoctoral fellow; C.I.B. and Y.N.J. are investigators of the Howard Hughes Medical Institute.
PY - 2004/2
Y1 - 2004/2
N2 - We developed a method for systematically comparing gene expression patterns across organisms using genome-wide comparative analysis of DNA microarray experiments. We identified analogous gene expression programs comprising shared patterns of regulation across orthologous genes. Biological features of these patterns could be identified as highly conserved subpatterns that correspond to Gene Ontology categories. Here, we demonstrate these methods by analyzing a specific biological process, aging, and show that similar analysis can be applied to a range of biological processes. We found that two highly diverged animals, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, implement a shared adult-onset expression program of genes involved in mitochondrial metabolism, DNA repair, catabolism, peptidolysis and cellular transport. Most of these changes were implemented early in adulthood. Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and MRNA degradation.
AB - We developed a method for systematically comparing gene expression patterns across organisms using genome-wide comparative analysis of DNA microarray experiments. We identified analogous gene expression programs comprising shared patterns of regulation across orthologous genes. Biological features of these patterns could be identified as highly conserved subpatterns that correspond to Gene Ontology categories. Here, we demonstrate these methods by analyzing a specific biological process, aging, and show that similar analysis can be applied to a range of biological processes. We found that two highly diverged animals, the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster, implement a shared adult-onset expression program of genes involved in mitochondrial metabolism, DNA repair, catabolism, peptidolysis and cellular transport. Most of these changes were implemented early in adulthood. Using this approach to search databases of gene expression data, we found conserved transcriptional signatures in larval development, embryogenesis, gametogenesis and MRNA degradation.
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U2 - 10.1038/ng1291
DO - 10.1038/ng1291
M3 - Article
C2 - 14730301
AN - SCOPUS:0842267618
SN - 1061-4036
VL - 36
SP - 197
EP - 204
JO - Nature Genetics
JF - Nature Genetics
IS - 2
ER -