Gene expression databases


We have produced a database of stem cell microarray data (StemBase) describing gene expression in more than 200 samples of stem cells and their derivatives in mouse and human. We illustrated how to use these data to study stem cell biology at three levels: cells, genetic networks, and particular genes [1]. Since the initial publication, updates of the database include, beyond the addition of new samples, novel querying mechanisms [2] and the use of the UCSC Genome Browser to display the data in genomic context [3].


CellFinder is a repository of molecular data associated to mammalian cells including images, gene and protein expression, and literature derived marker information [4]. The database includes tools to navigate cells and tissues organized as a hierarchy, and to compare and browse the stored data.


[1] Perez-Iratxeta, C., G. Palidwor, C.J. Porter, N.A. Sanche, M.R. Huska, B.P. Suomela, E.M. Muro, P. Krzyzanowski, E. Hughes, P.A. Campbell, M.A. Rudnicki and M.A. Andrade. 2005. Study of stem cell function using microarray experiments. FEBS Letters. 579, 1795-1801.

[2] Porter C.J., G.A. Palidwor, R. Sandie, P.M. Krzyzanowski, E.M. Muro, C. Perez-Iratxeta, M.A. Andrade-Navarro. 2007. StemBase: a resource for the analysis of stem cell gene expression data. Methods Mol. Biol. 407, 137-148.

[3] Sandie, R., G.A. Palidwor, M.R. Huska, C.J. Porter, P.M. Krzyzanowski, E.M. Muro, C. Perez-Iratxeta, M.A. Andrade-Navarro. 2009. Recent developments in StemBase: a tool to study gene expression in human and murine stem cells. BMC Research Notes. 2, 39.

[4] Stachelscheid, H., S. Seltmann, F. Lekschas, J.F. Fontaine, N. Mah, M. Neves, M.A. Andrade-Navarro, U. Leser and A. Kurtz. 2013. CellFinder: a cell data repository. Nucleic Acids Research. 42, D950-D958. [CellFinder]