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We use ChIP-seq data from the highly standardized ENCODE project [16] so we expect minimal noise in the source data due to differences in experimental procedures between the cell line datasets.
Analysis of two cell line datasets with treatment response data indicated that subtypes respond differently to targeted compounds.
Pathway analysis revealed similar patterns of enriched pathways from differentially expressed genes of both human clinical and cell line datasets.
Jang et al. (2014) and Papillon-Cavanagh et al. (2013) compare the performance of various machine learning methods applied to the cancer cell line datasets.
Hence, the percentage intersection between zebrafish and human cancer cell line datasets were more than half of the percentage intersection among the human cancer cell lines.
The mRNA level of MMP-9 in 51 breast cancer cell lines were also studied using publically available microarrays and mRNA sequencing breast cancer cell line datasets [ 18].
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The Entrez Gene identifier was used for mapping genes from the NSCLC cell line dataset to those from the human NSCLC tumor and MCF-7 profile datasets.
These results indicate that the cell line dataset largely reflects the gene expression pattern for TCF/LEF regulated genes in both the cell line and the cancer tissue.
To illustrate this, a previous study of correlations in the NCI-60 dataset was unable to find any correlations reaching significance [17], while our permutation method did (see "Analysis of a cancer cell line dataset", in Results).
Interestingly, all three of the genes evaluated in this study that were highlighted in the previous study as having a strong correlation between hypermethylation and expression showed a similar negative correlation in our cell line dataset (MGMT: −0.63, RBP1: −0.78, IGSF4: −0.69).
RHB and SJS generated the human keratinocyte cell line dataset.
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