Table 2 |
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|
Summary of Input, analysis, output for each dimension |
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|
'Omics classification |
Assay(s) measured |
Input |
Functionality*** |
Output |
|
|
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|
Genomics |
Copy number |
Array CGH |
Segmentation Direct thresholding Moving average-based thresholding Z-transformation of moving average Whole genome visualization |
Regions of gain and loss Gene lists for further analysis High-resolution karyogram images Frequency histograms |
|
Genomics |
LOH |
SNPs* |
LOH based on consecutive altered markers |
Regions of LOH |
|
Genomics |
LOH |
Microsatellite markers |
Same as above |
Same as above |
|
Genomics |
Copy number, LOH |
Identify regions of uniparental disomy (UPD): LOH with no copy number change |
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|
Epigenomics |
DNA methylation |
MeDIP + array CGH |
Direct thresholding Moving average-based thresholding Z-transformation of moving average |
Regions of enrichment and lack of methylation Gene lists for further analysis |
|
Epigenomics |
DNA methylation |
Bilsulphite-based |
Visualization against genome position Thresholding of proportion of methylated CpG's |
|
|
Epigenomics |
Histone modification states |
ChIP-on-chip |
Direct thresholding Moving average-based thresholding Z-transformation of moving average |
Regions of enrichment and lack of enrichment Gene lists for further analysis |
|
Epigenomics |
DNA methylation, Histone modification states |
Epigenetic interplay |
Regions of mutually exclusive change between chromatin state and DNA methylation |
|
|
Transcriptomics |
Gene expression** |
Microarrays |
Heatmap visualization, clustering Histograms Statistical comparisons |
Expression of genes of interested based on DNA analysis |
|
Transcriptomics |
Gene expression** |
SAGE |
Heatmap visualization, clustering Histograms Statistical comparisons |
Expression of genes of interested based on DNA analysis |
|
Genomics, Transcriptomics |
Copy number, Gene expression |
Correlation analysis of copy number and expression Statistical comparison of expression in regions of copy number difference (two group analysis) |
Genes whose expression is strongly regulatd by copy number p-values for associations p-values for group comparison |
|
|
Genomics, Epigenomics |
Copy number, DNA methylation |
Identify regions of concerted change in BOTH copy number and methylation ("two-hit") Identify regions with change in copy number OR DNA methylation |
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|
Genomics, Epigenomics |
LOH, DNA methylation |
Identify allele-specific methylation events |
Regions of allele specific aberrant methylation |
|
|
Genomics, Epigenomics, Transcriptomics |
Copy number, LOH, DNA methylation, Histone modification Gene Expression |
Identify co-ordinate genetic, epigenetic and gene expression changes |
Genes altered at multiple levels |
|
|
|
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|
* Affymetrix and Illumina data must be pre-processed prior to import; ** functionality invoked in the context of genetic and epigenetic data analyses; ***aligned to genome features (Database of genomic variants, CpG Islands, microRNAs etc.) |
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|
Chari et al. BMC Bioinformatics 2008 9:422 doi:10.1186/1471-2105-9-422 |
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