Table 2 Summary of Input, analysis, output for each dimension

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

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

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