Unable to display cell lines from a custom list in graphs
I uploaded a custom list to the graphing page in the explore your data section, but there doesn’t seem to be anything I can do with these cell lines after that. There are no options to display or...
View ArticleDefinition of common essential genes
In the web portal, common essential genes are defined as: A gene which, in a large, pan-cancer screen, ranks in the top X most depleting genes in at least 90% of cell lines. X is chosen empirically...
View ArticleViability test used?
If I knocked down the “A” gene using technologies such as RNAi, in two cell lines with opposite dependencies for that gene, how can I evaluate the different dependency? Would a difference in cell...
View ArticleUser drug sensitivity (PRISM Repurposing Primary screen)
Hello, What do the values in this mean? Log2 ic50? 2 posts - 2 participants Read full topic
View ArticleProteomics vs Public expression data
Hey everyone. I’ve run queries of CRISPR / RNAi scores vs Proteomics / Public expression for a few genes. I’ve noticed that the hits for Proteomics and Public expression do not seem to be very...
View ArticleRe-distribution of the CCLE data (Licensing)
Hey everyone, I was wondering about the licensing of DepMap, especially CCLE. Am I allowed to re-distribute the dataset on another website? Best, Judith 2 posts - 2 participants Read full topic
View ArticleCoDependencies - Full List and Significance
I have some basic questions about co dependencies. How do I get the full list of genes which have codependency scores? Looking for more than 100. What is meaningful? I would nit consider a correlation...
View ArticleCell line selection
Hi, I need to select a cell line of specific cancer with specific gene amplification. How do I do that. I tried using cell line selector, I am not understanding which cell line has maximum expression....
View ArticleRNA mutation data
Dear DepMap, In the Gandhi et al Nature publication from 2019, there is mention of somatic mutation calling from RNA-Seq. I am unable to find that information on DepMap or the CCLE home page. Is this...
View Articledataset for abundance of transcripts?
I am looking for a dataset to know abundance of different gene transcripts. I searched through the datasets available on depmap and found this? Is this the right dataset to use to answer this...
View ArticleTotal number of cancer dependency genes / proteins across all cancer cell lines
Hi, is there any easy way to find the total number of cancer dependency genes / proteins across all cancer cell lines or a rough approximation as of 2024? 1 post - 1 participant Read full topic
View ArticleA simple question about Gene expression and CRISPR Gene effect
Hi everyone! I’m an undergraduate doing research based on gene expression and CRISPR gene effect data in Depmap. When I combine the expression and gene effect data together, I found various genes that...
View ArticleAbout PREDICTABILITY
After reading your introduction document, I still have questions about PREDICTABILITY. I’m curious if a higher PREDICTABILITY implies higher confidence in the numbers obtained from this CAS9...
View ArticleSuggestion for cell line information
It is better to make cell line name and ID come together. 1 post - 1 participant Read full topic
View ArticleMutation reporting criteria
The mutations detected in the HRD test do not match the DNA mutation information reported in Depmap. Could you provide the criteria for registering mutations in Depmap? 2 posts - 2 participants Read...
View ArticleProteome data access
Hey, I was trying to download proteome data on the portal, but the matrix I got was absent of any protein quantity. I am pretty sure I’ve downloaded proteome data of Gigi’s lab from Depmap before. Not...
View ArticleResponse to compound in different cell lines
Hi, I am very interested in the data that shows the response of different cell lines to specific compound. I would like to know more about the log2 fold change showed in the result. What parameter did...
View ArticleHash code for each unique file downloaded
Hello DepMap team! This is more a request than a bug, I think. It is just I am not capable to find any info about how to get the hash code of each dataset I downloaded. I reported this request also...
View ArticleQuestion about segtab annotations in ABSOLUTE CN file
Hi there, I am looking at ABSOLUTE CN calls from this file: DepMap Data Downloads I am a little confused with regards to how to interpret the columns labeled “Cancer_call_frac_a1” and...
View ArticleDrug sensitivity data availability
I am wondering if the AUC values that were available on the 21Q4 version but not available in today’s version for drugs from CTRPv2 and PRISM were redacted due to quality filtering or if it is a...
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