Ccle Cell Lines- Expression Data-Rma Log2Ratio

Question

[Hmm]

Can someone please help me understand how can i interpret the expression values of the genes in the CCLE expression dataset:

http://www.broadinstitute.org/ccle/data/browseData?conversationPropagation=begin

look at file: CCLE_Expression_Entrez_2012-09-29.gct

It says the data is:

Gene-centric RMA-normalized mRNA expression data.

or when i look at a single gene the y axis of the plot says:

the mRNA expression level (RMA,log2ratio)

How do i know which gene is upregulated in the celline and which is down regulated? Any help/direction is really appreciated. Thanks.

[Neilfws]

Link to the data or some other resource please? That file name alone is no use. Where are these gene plots?

[Hmm]

@Neilfws : i have updated the post. thanks

Answer 1

[Ashutosh Pandey]

The y-axis represents the expression and the x-axis different cell types. The expression here is shown as a box plot (See this http://en.wikipedia.org/wiki/Box_plot) with the solid black line as a mean expression of that gene for that particular cell type. RMA Normalisation was used to normalise the expression and then the data was converted to log2. This means difference of 1 unit on the y-scale will correspond to 2 fold expression difference between two cell-types. Let me know if you have a specific question.

[Hmm]

Thanks for responding. What if i didnot have many cellines to compare with and only had one cell line. So what does that mean for the gene. Is it up or down? what are we comparing to for up and down with in a celline? How can i say that a gene is overexpressed or under expressed? I really appreciate your help.

[jdittmar]

Any answer on this? Did you figure out how to interpret over/under expression?