Hi, I’d like to check the expression level of genes using the RNAseq data from CCLE. However, I only see the gene ID in the file without the corresponding transcript ID, making it difficult to understand which isoform has been used for the analysis. May I know the criteria of picking transcript for this analysis? Many thanks!
Thanks for reaching out!
I am assuming you are using OmicsExpressionProteinCodingGenesTPMLogp1.csv in the “primary files” section in the download page. It contains RSEM’s gene-level abundance estimates which are essentially a summary of all isoforms for each gene. If you want to see transcript-level abundance estimates, you should be able to download OmicsExpressionTranscriptsExpectedCountProfile.csv in the “all files” section which contains expected counts on the transcript level. Hope this helps!