Understanding Biology Using Gene Expression Profiling
Division of Biology, California Institute of Technology
2005. 2. 24
We have the capacity to fabricate mouse whole genome cDNA and oligonucleotide microarrays (32K). Transcriptional analysis of the mouse primary B cell single/double ligand screen with 33 ligands was carried out. The data suggested interesting crosstalk in the signaling pathways downstream of the proliferative ligands. B cells derived from human Bcl2 transgenic mice have sustained survival in culture, and their transcript profile was studied. We have analyzed transcriptional changes after the addition of single/double ligands in the macrophage cell line RAW264.7. A time series examining the effects of the combinations of LPS/IFN¥ã, LPS/2MA, LPS/PGE2 and LPS/ISO enabled identification of the signal networks between them. In addition, we found that caspase 6 is involved in enhanced T cell proliferation lacking the p85¥â subunit of phosphoinositide 3-kinase. We have examined the effects on RAW cells transfected with lentiviral shRNA, siRNA or antisense oligonucleotide. The macrophage J774 cells lacking G¥â1/2 subunits by RNA silencing machinery modulated all GPCR-mediated cellular responses and blocked the gene expression induced by PGE2, ISO or UTP but not by LPS. A bioinformatics analysis of memory consolidation also revealed involvement of the transcription factor c-Rel. In current biology, biological processes of interest are studied as complex systems of functionally interacting macromolecules. Systems biological approaches using DNA microarray and bioinformatics-related tools are ideal to accelerate the identification of the genes and to describe the signaling pathways between them so that complex biological phenomena and systems can be understood coordinately.
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