Hello, I am attempting to use the “Custom Downloads” feature with a custom gene list to download proteomics data. The produced excel file contains no data and has the file title, “Proteomics_subsetted_NAsdropped”. I have tried multiple browsers and changing the list of genes with no success. If I download the data set without a gene filter it downloads all the unfiltered data successfully. The custom gene list I am using works for all data sets except for proteomics data. Does anyone have this issue and/or know a fix? Thanks for your time.
I did some an investigation and the issue appears to be that the custom download only supports filtering by genes datasets such as CRISPR, RNAi, expression, CN, etc which have “gene” as the features.
When the filter by “gene” is applied, it only includes features which are type “gene” and match entrez ID to the genes entered. As a result, it ignores all features which are of type “protein”.
We could improve the current filter to understand that association between proteins and genes, but today it’s missing that logic. (I’ll put that in our tracker a possible future improvement for custom downloads.)
So, to answer your question, yes, this appears to be an issue in custom downloads.
The only workaround I can think of suggesting is that you could use “Cell line selector” to extract the features if you only have a handful of genes you want data for. (There’s a fair amount of clicking required, so it’d be tedious to extract many this way.)
The Cell line selector tool allows you to add feature tracks to your list of cell lines and then download the resulting table. (When you add a feature in cell line selector, the drop down widget does understand the mapping between genes and proteins, so it’s able to find features in the proteomic dataset.)
Once you’ve added all of the proteins you’re interested in, you can download the table by using the “download” icon in the lower left.
Thanks for your reply and suggestions. I’ll try the cell line selector tool out.