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It should be noted that it was not feasible to directly assess the potential role of intrauterine factors, for example, by means of analysis of pattern of genome expression in lymphocytes obtained from cord blood samples.
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However, the studies on autopolyploidization aimed at identifying the alterations of genome expression patterns are relatively less than those on allopolyploidization.
For example, microarray analyses in allotetraploid cotton have shown that various tissues exhibit a pattern of parental genome expression described as "genomic dominance" (over-expression of one parental genome relative to the other when compared to the ancestral expression state of both diploid parents) [ 14, 17, 19].
We have also previously profiled the temporal pattern of genome wide expression in response to the heat shock induced hlh-1 transgene used for ChIP-chip in this study [5], [6]; taking genes identified as up-regulated by hlh-1 over expression 6 hours after induction resulted in a list of 927 genes.
The non-random arrangement of genes in the genome is intimately connected to the pattern of gene expression across the genome [ 1].
To understand patterns of therapy response genome expression profiling and detection of genetic polymorphisms enables to identify key mechanisms in systems biology.
GEDI is a "Self Organizing Map" based software that allows the visualization of whole genome expression patterns in mosaics of n × m tiles.
Furthermore, although many polyploid species have formed repeatedly, patterns of genome evolution and gene expression are largely unknown for natural polyploid populations of independent origin.
Our main objectives were to: 1) investigate the genomic changes and expression differences of parental homeologs in T. mirus relative to its diploid parents, 2) determine the identity of the genes that exhibit those changes, and 3) assess whether individuals within and among recurrently formed natural populations of T. mirus show similar patterns of genome evolution and gene expression.
Finally, the pattern of genome-wide hypermethylation and DNMT3b over-expression combined with tissue cadmium levels may provide biomarkers to specifically identify cadmium-induced human prostate cancers.
Generally, this work demonstrates the potential to discover genes de novo and examine genome-wide patterns of gene expression in a highly tissue-specific manner in organisms that lack a sequenced genome.
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