Methods, tools, systems and computer readable media for analyzing CGH data, together with data from an independent source. Independent data is compared with the CGH data, wherein the CGH data is characterized by sets of defined regions differentiated by at least one property. Enrichment is assessed for at least one subset of the data from an independent source with regard to at least one of the sets of defined regions in the CGH data. Methods, tools, systems and computer readable media for visualizing CGH data as it is impacted by data from an independent source are also provided. A relationship between at least one defined set of the CGH data and at least one set of sequence elements defined in the data from an independent source may be visualized.