when searching gene > characterization > Methylation 1kb TSS . From searching my gene of interest it appears that data is based on the old GRCh37/hg19 (2009)? since the coordinates don’t match with promoter from version GRCh38/hg38 is this possible?
Same question for CpG data. It would be great if information of genome version be included somewhere.
Also it would be great to have somewhere a guide on abbreviations for those not familiar. For instance when downloading Translocation data , there is a column lableled Cosmic fus , I assume is about the Sanger Cosmic database and whether there is a fusion but what does True or False means exactly , fusion not found in Cosmic? false ? . Same for meaning of Multi Sv Fusion. That is why a help menu with abbreviations would be great.
Thank you in advance for your help
Yes, that’s quite likely. The quarterly data updates that DepMap produces are now using hg38. However the Methylation data is not part of those datasets. It was generated earlier as part of the CCLE project and I believe all of that data was based on hg19. The paper cited for this data (we list papers on the download page https://depmap.org/portal/download/?release=CCLE+2019 ) confirms that hg19 was used for the methylation data.
The translocation data was also published with the same paper, but I don’t see any mention of cosmic_fus in the paper (https://www.nature.com/articles/s41586-019-1186-3). I may need to reach out to the original authors to find where they published the definitions of those columns.