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The success of our method is mainly due to the integrated use of multiple genomics data.
There is no direct way to integrate multiple genomics data such as protein protein interactions and expression from perturbation experiments in current implementations.
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The importance of integrating multiple genomics information has been well recognized by the research community.
Multiple functional genomics data for complex human diseases have been published and made available by researchers worldwide.
Systems biology approaches can help genomics studies through systematic and integrative approaches to incorporate multiple genomic data and assemble the information toward cellular or physiological behaviours related to a particular biological phenotype such as disease.
Large-scale cancer genomics projects such as TCGA (The Cancer Genome Atlas Research Network) are currently generating multiple layers of genomics data for each tumor, including DNA copy number, methylation, and mRNA expression, which provide a great opportunity for systematic modeling of dysregulated transcription.
Lastly, we analyzed the NHLBI GO Exome Sequencing Project Kabuki dataset, a congenital disorder affecting multiple organs and often intellectual disability, contrasted with Complete Genomics data as controls.
Therefore, human protein characterization efforts that focus on similar proteins across multiple organisms are expected to more effectively capitalize on the available genomics data.
The iBBiG bi-clustering algorithm is optimized for module discovery in sparse noisy binary genomics data and can be used for meta-GSA of multiple genomics datasets, to discover modules: groups of phenotypes whose differential gene expression profiles are enriched in the same gene sets.
The heatmaps in Gitools can contain multiple dimensions, that is, multiple values in each cell, which makes it especially well suited to the exploration of multidimensional cancer genomics data.
More recently, population genomics data from sequencing [14] and microarray analysis [15] of multiple individuals of the same species have added a third level of sequence divergence.
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