Biomedical subjects

Judith M Boer

Publications and source records attributed to Judith M Boer.

3 recordsLinked to original sources

PubMed2003

GeneHopper: a web-based search engine to link gene-expression platforms through GenBank accession numbers.

Global gene-expression analysis is carried out using different technologies that are either array- or sequence-tag-based. To compare experiments that are performed on these different platforms, array probes and sequence tags need to be linked. An additional challenge is cross-referencing between species, to compare human profiles with those obtained in a mouse model, for example. We have developed the web-based search engine GeneHopper to link different expression resources based on UniGene clusters and HomoloGene orthologs databases of the National Center for Biotechnology Information (NCBI).

Animals↗

PubMed2002

A common reference for cDNA microarray hybridizations.

Comparisons of expression levels across different cDNA microarray experiments are easier when a common reference is co-hybridized to every microarray. Often this reference consists of one experimental control sample, a pool of cell lines or a mix of all samples to be analyzed. We have developed an alternative common reference consisting of a mix of the products that are spotted on the array. Pooling part of the cDNA PCR products before they are printed and their subsequent amplification towards either sense or antisense cRNA provides an excellent common reference. Our results show that this reference yields a reproducible hybridization signal in 99.5% of the cDNA probes spotted on the array. Accordingly, a ratio can be calculated for every spot, and expression levels across different hybridizations can be compared. In dye-swap experiments this reference shows no significant ratio differences, with 95% of the spots within an interval of +/-0.2-fold change. The described method can be used in hybridizations with both amplified and non-amplified targets, is time saving and provides a constant batch of common reference that lasts for thousands of hybridizations.

Cells, Cultured↗

PubMed2002

Expression profiling in stably regenerating skeletal muscle of dystrophin-deficient mdx mice.

The mdx mouse is comparable to Duchenne muscular dystrophy in having an absence of dystrophin. While dystrophic human skeletal muscle undergoes progressive degeneration, in the mdx mouse regeneration and tissue remodeling substantially compensate for the lack of dystrophin. To better understand the molecular events leading to active muscle regeneration in mdx muscles, we have determined the gene expression profiles of wild-type and mdx hind limb muscles using oligonucleotide arrays. Compared to wild-type, 58 genes were found to be differentially expressed in mdx. The molecular signature of actively regenerating skeletal muscle in young adult mdx mice showed upregulation of muscle development genes and genes involved in immune response, proteolysis and extracellular matrix remodeling. Moreover, energy metabolism and mitochondrial function were not compromised. Insights into the processes activated in the mdx muscle to compensate for chronic degeneration may have important implications for therapy in patients with muscular dystrophy.

Animals↗