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I'm trying to retrieve the most expressed genes from a cell line from the NCI-60, lets say cell line NCI-H23, but I'm not sure where to find the gene expression data. My main goal is to create a network using that data and iRefIndex to be loaded into Cytoscape. Does anyone know where I can find the correct data or guide me in the right direction?

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CellMiner portal has plenty of data about NCI-60 cell lines, inclusive microarray gene-expression.

Also, NCI-60 is a subset of the ~1000 cell lines covered by the GDSC project for which you have multiple types of measurements (e.g. copy-number, mutation, gene-expression).

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Cosmic Cell Lines Project provides gene expression data for 1000+ cell lines (including NCI-60 panel together with NCI-H23 cell line). For each gene in a cell line, you can get Z-score and over/under-expression status calculated across all tumor samples diploid for that gene.

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