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Sci. Signal., 9 December 2008
Vol. 1, Issue 49, p. ra16
[DOI: 10.1126/scisignal.1163630]

RESEARCH ARTICLES

Analysis of Metagene Portraits Reveals Distinct Transitions During Kidney Organogenesis

Igor F. Tsigelny1,2*{dagger}, Valentina L. Kouznetsova3{dagger}, Derina E. Sweeney3, Wei Wu3, Kevin T. Bush3, and Sanjay K. Nigam3,4,5,6*

1 Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093–0505, USA.
2 San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093–0505, USA.
3 Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093–0693, USA.
4 Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093–0693, USA.
5 Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093–0693, USA.
6 John and Rebecca Moores UCSD Cancer Center, School of Medicine, University of California, San Diego, La Jolla, CA 92093–0693, USA.

{dagger} These authors contributed equally to this work.

Abstract: Organogenesis is a multistage process, but it has been difficult, by conventional analysis, to separate stages and identify points of transition in developmentally complex organs or define genetic pathways that regulate pattern formation. We performed a detailed time-series examination of global gene expression during kidney development and then represented the resulting data as self-organizing maps (SOMs), which reduced more than 30,000 genes to 650 metagenes. Further clustering of these maps identified potential stages of development and suggested points of stability and transition during kidney organogenesis that are not obvious from either standard morphological analyses or conventional microarray clustering algorithms. We also performed entropy calculations of SOMs generated for each day of development and found correlations with morphometric parameters and expression of candidate genes that may help in orchestrating the transitions between stages of kidney development, as well as macro- and micropatterning of the organ.

* To whom correspondence should be addressed. E-mail: snigam{at}ucsd.edu (S.K.N.) and itsigeln{at}ucsd.edu (I.F.T.)

Citation: I. F. Tsigelny, V. L. Kouznetsova, D. E. Sweeney, W. Wu, K. T. Bush, S. K. Nigam, Analysis of Metagene Portraits Reveals Distinct Transitions During Kidney Organogenesis. Sci. Signal. 1, ra16 (2008).

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