I'm wondering is there a way to calculate the differentially expressed genes in cancer cell lines(e.g.,MCF7)? The gene expression data (microarray or RNA-seq) for cancer cell lines can be found in many projects, but corresponding normal cell does not exist. Is it sound to use the corresponding normal tissue(e.g.,breast) gene expression for the calculation, such as the Illumina Body Map? Or is there any project to characterize the genome features of these cancer cell lines?
1 answer
Fairly obviously, the best method to get a sound comparison would be to generate the data yourselves and make the comparison there were you can control for design elements.
Short of that, using a tissue is problematic because of cell type heterogeneity although it may give you a basic idea of what effect you may expect. I would not make any biological claim comparing to breast tissue; you will need the exact cell type. However, you could use it to see if further analysis is justified.
I'm unsure what you're looking for in 'a project to characterize the genomic features of these cancer cell lines'. Can you be more specific?
If you only need them to identify a list of candidate genes, I think that may work. If you wanted to say that those sites are definitively differentially-expressed in cancer cells, you'll need to have the cell types matched. Otherwise you'll introduce a lot of false positives due to cell type effects
Log in to answer this question.
-
How to retrieve RNA expression dataset of METABRIC - 144 adjacent normal samples ?
written by pooja •
-
Differential Gene Expression Using Deseq2
written by mropri
-
Any database for downloading cancer cell-lines transcriptome differential expressed gene (DEG) list…
written by chiefcat
-
Transformed cancer cell-lines RNA-seq database
written by ever_wudi •
-
Gene expression comparison of Cancer and Normal tissue
written by evocanres •
-
News: Cell Lines: multi-omics network of associations to model precision treatment
written by Pine Biotech •
-
Gold standard cell lines with characteristic gene fusions for Breast Cancer
written by manali.rupji •
-
why no replicate samples in ccle mRNA data
written by liuyang •
-
How to compare the gene expression signature of treated cancer cell and normal cell
written by liuyang •
-
Comprehensive Annotation Of Luminal/Basal For Breast Cancer Cell Line Microarray
written by user
