So I have to list my cell lines for TNBC and I was searching for the expression of CEBPB in MD MB 231 cell for tnbc . In the characterization option I saw that cebpb is not being expressed in the MD MB 231 cell line but in the protein atlas there is expression of the gene in the MD MB 231 cell line .I was wondering if I can see the raw data for the values of TPM taken by depmap so that I can get an idea ?
Hi,
We provide expression expected count data on both gene- and transcript-level. If you navigate to the file downloads page, you should be able to access OmicsExpressionGenesExpectedCountProfile.csv and OmicsExpressionTranscriptsExpectedCountProfile.csv, respectively.
Hope this helps,
Simone
Hi so I checked the gene by the transcript id ENST00000303004 and its not present in the csv data. Do you know any possible reasons for this ? .It has 3 isoforms as well , is it the reason that’s its not present there??
By csv data, do you mean OmicsExpressionTranscriptsExpectedCountProfile.csv? I see a column called “CEBPB (ENST00000303004)” in this file, and a column called “CEBPB (ENSG00000172216)” in OmicsExpressionGenesExpectedCountProfile. Is either of these what you are looking for?
Oh yes!!! that’s the gene I am lookin for , but when I am typing the gene name in the excel file , its showing they couldn’t find it. Can you please tell me how to troubleshoot it or send the screenshot of the CEBPB gene in both the csv files ?
The files are quite large so I suspect excel is probably not able to handle a search like this. I’d highly recommend parsing these data frames programmatically.
I am very much new to bioinformatics so I couldn’t understand what you are suggesting. Can you please simplify as to how it will be easy for me to the check the tpm values of the gene CEBPB ?
One way to programmatically read data frames is using pandas in python. I’d suggest checking out this tutorial: Read csv using pandas.read_csv() in Python - GeeksforGeeks
