Dissertation/Thesis Abstract

Identification of putative targets of Nkx2-5 in Xenopus laevis using cross-species annotation and microarray gene expression analysis
by Breese, Marcus R., Ph.D., Indiana University, 2011, 200; 3491457
Abstract (Summary)

The heart is the first organ to form during development in vertebrates and Nkx2-5 is the first marker of cardiac specification. In Xenopus laevis, Nkx2-5 is essential for heart formation, but early targets of this homeodomain transcription factor have not been fully characterized. In order to discover potential early targets of Nkx2-5, synthetic Nkx2-5 mRNA was injected into eight-cell Xenopus laevis embryos and changes in gene expression measured using microarray analysis. While Xenopus laevis is a commonly used model organism for developmental studies, its genome remains poorly annotated. To compensate for this, a cross-species annotation database called CrossGene was constructed. CrossGene was created by exhaustively comparing UniGene transcripts from Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus, Xenopus laevis, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans using the BLAST family of algorithms. Networks were then assembled by recursively combining reciprocal best matches into groups of orthologous genes. Gene ontology annotation from all organisms could then be applied to all members of the reciprocal group. In this way, the CrossGene database was used to augment the existing genomic annotation of Xenopus laevis. Combining cross-species annotation with differential gene expression analysis of Nkx2-5 overexpression led to the discovery of 99 potential targets of Nkx2-5.

Indexing (document details)
Advisor: Edenberg, Howard J.
Commitee: Hurley, Thomas D., Rhodes, Simon J., Skalnik, David G.
School: Indiana University
Department: Biochemistry and Molecular Biology
School Location: United States -- Indiana
Source: DAI-B 73/05, Dissertation Abstracts International
Subjects: Molecular biology, Bioinformatics, Developmental biology
Keywords: Bioinformatics, Cardiogenesis, Gene ontology annotation, Genomics, Homology, Microarrays, Nkx2-5
Publication Number: 3491457
ISBN: 9781267138026
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