Jeffrey, this may help to answer your question:
journals.bmn.com
(free registration will give you full access until September 1st)
Serial analysis of gene expression: from gene discovery to target identification
Stephen L. Madden, Clarence J. Wang and Greg Landes
Drug Discovery Today 2000, 5:415-425
Genzyme Molecular Oncology and Genzyme Corporation, PO Box 9322, Framingham, MA 01701-9322, USA
A few excerpts:
SAGE is heralded as an unbiased and comprehensive high-throughput transcript profiling technology and is therefore ideally suited for novel pathway elucidation. As with any attempt at pathway elucidation utilizing transcript profiling, transcriptional changes caused by a single or a few gene changes in an otherwise isogenic background potentially provides few transcriptional differences and therefore the data output is fairly straightforward to interpret. SAGE has been applied in this way towards elucidating transcriptional manifestations within cells harboring functional or non-functional p53
and, synergy with DNA microarrays a la AFFX:
The dilemma that has evolved from many large complex disease transcriptome analyses is that further verification efforts are necessary to limit the pool of potential candidate genes. The wealth of possible disease-specific genes that have been revealed by SAGE ( Ref. 17) in the cancer arena necessitates a verification platform to aid in limiting the time-consuming functional work downstream from data generation. cDNA microarrays are currently being formulated by utilizing SAGE data to program the target array, which will ultimately be interrogated by additional samples. This approach is more advantageous than using prefabricated cDNA or oligomer arrays where only previously defined cDNAs can be interrogated, omitting novel genes that could be relevant to the specific disease being investigated. SAGE tags that do not correspond to known genes or ESTs, and which therefore could represent novel genes, can be used effectively to amplify additional sequences from cognate cDNAs ( Ref. 14 describes this approach). This facilitates the integration of potentially novel cDNAs into the design of SAGE-defined microarrays. This approach of SAGE-based custom microarrays has been used to identify genes that were differentially expressed in primary and metastatic breast cancer 21
Other techniques I have heard mentioned are TOGA ncbi.nlm.nih.gov, as well as things with names like RADE (rapid analysis of differential gene expression) or GeneCalling used by the likes of MLNM, CRGN, etc. LYNX also has described some work along similar lines. I am not qualified to comment on the merits of any of these.
PB |
