Pathway maybe don't descript the disease state.
Chi Lee
Wednesday, 31 October 2007 16:20 UTC
Who can tell me how to insert my image to my blog?
KEGG and Genmapp can often be queried to find interaction between protein and protein. In fact, many of researcher regard mRNA test value by microarray or Real time PCR as protein test value. When ratio of difference mRNA value in microarray is combined over group of genes within some pathways, puzzle map appears.
. (From Genmapp). Please pay attention to SMAD4 and CDKN1A in the map. Blue boxes denote downexpression of gene. Red boxes denote overexpression of gene. Who can tell me which is the effect of SMAD4 to CDKN1A. Activity? or Inhibition? Even though I have observed thousands of map which was combined microarray data to KEGG or Genmapp, none of map can put a clear interpretation on the relation among genes in upstream and downstream from comparison between some groups of microarrays. According to reference lists of KEGG, I understood the action between one gene and other gene is local optimality in the special experient conditions, such as cultured 3T3 cell at experience. In another special trial by gene expression microarray, new relatonship of genes respond to the trial. With combining microarray data to the pathway of KEGG or Genmapp, the majority of genes have not been assigned to a definitive pathway (From Han-Yu Chuang et al. Network-based classification of breast cancer metastasis). You can also think the resource of mismatch phenomenon is the difference of gene relation between local optimality and global optimality.
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