Data Availability for Drugs used in PRISM Screens
Dear DepMap Community, I am interested in obtaining some information on the drugs that were used in the PRISM screens which are available on DepMap. I am looking for drug information for the screens -...
View Article12015 genes with protein data
Dear Team, I have identified 12,015 genes with protein data in DepMap. The absence of protein data for the remaining genes is likely due to their relatively low abundance. Could there be any other...
View ArticleProblem to map drug info to 24Q2_Extended_Primary_Data_Matrix
When I tried to map the drug info from the file “Repurposing_Public_24Q2_Extended_Primary_Compound_List.csv” to the data matrix file “Repurposing_Public_24Q2_Extended_Primary _Data_Matrix.csv”, I...
View ArticleExpression data
Within a certain cell line from the batch corrected expression dataset, how do I know if a gene is upregulated or underregulated from the counts provided. Thanks! 1 post - 1 participant Read full topic
View ArticleUnable to download anything from dep,ap
Is there something wrong with the portal. I get the following error message: AccessDenied Request has expired 10 2024-08-28T18:57:08Z 2024-08-28T18:58:12Z HQAMYTZ4G08S6TMR...
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Trouble visiting the DepMap portal
Hello! Unfortunately, I have some problems visiting the DepMap portal. The navigation menu has a strange appearance (as can be seen in the figure). Additionally, some features of the portal are not...
View ArticleHow to plot a specific gene effect vs different cell lines in DepMap?
For example gene name gene effect on the y-axis and then cell lines as points (Cell lines are in two categories). I am especially struggling on where to find this information. 1 post - 1 participant...
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What's the difference between 'cutaneous melanoma' and 'melanoma'?
Dear community, Hi, I have a question about the subtypes of melanoma in the Celligner. When I checked the subtypes of melanoma, I found that there are confusing words; cutaneous melanoma and melanoma....
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Contrasting Gene Effects between RNAi and CRISPR of CCN4
“Hi, I am currently using the web portal data explorer to investigate the gene effect of CCN4, but the results are puzzling me. Why do the outcomes of RNAi and CRISPR appear to be opposite? Of course,...
View ArticleRedundant, incompletely overlapping annotation of gene fusions
Hi, DepMap folks. I’m trying to use the DepMap 24Q2 Fusions dataset to identify cells with the BCR::ABL1 gene fusion, and I’ve noticed what looks like a mistake in the annotation: the dataset contains...
View ArticleCompound instance
What is the difference between ELOXATIN(BRD:BRD-K78960041-001-03-2) and ELOXATIN(BRD:BRD-K78960041-001-05-7) for Primary PRISM screen. The log 2 fold change values for them are pretty different even...
View ArticleNumber of screened compounds
For how many compounds does DepMap include publicly available sensitivity data and for how many cell lines? 1 post - 1 participant Read full topic
View Article24Q2 - PureCN Integer Copy Number for Chr X and Y
Hello, I am looking through the data release in 24Q2 and notice that the PureCN copy number profiles for both genes and segments do not have data for chromosome X and Y. Is there somewhere I can find...
View ArticleHow can I see the change in gene expression for several genes after the KO of...
Hello, I am currently looking for a way to see the post-perturbational expression of several Genes after the KO of the Arhgap25 in Leukemia cell lines. Is there any possibility to do that and if so it...
View ArticleDiscrepancy between two damaging mutation file from 23Q4
Hi DepMap team, I noticed a discrepancy between damaging_mutations.csv (downloaded from “Downloads/Custom Downloads” page) and OmicsSomaticMutationsMatrixDamaging.csv (downloaded from “Downloads/All...
View ArticleHow can I access/download large depmap datafiles without losing information?
Hi all! I was able to download and use the depmap library on R using BioConductor. Im trying to access the OmicsExpressionGenesExpectedCountProfile.csv, but the functions I tried to use don’t work. I...
View ArticlePlease recommend a user manual
Hi, I am a new user and would like to know whether DepMap has a user manual so that I can learn how to use this databases. Thank you so much. 1 post - 1 participant Read full topic
View ArticleSingle gene comparison between several cell lines
Hello, how can I compare/plot normalised expression levels of a single gene in several cell lines (three)? Differential expression analysis does not let me compare individual cell lines. Thanks! 1...
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Help plotting putative copy number alterations
Hi all! Can someone please help explain how I can make these types of plots? I cant figure out what to select in the data browser to make them for my genes of interest. Thank you!!! 1 post - 1...
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The web page cannot be displayed properly
Firstly, thank you very much for providing this database for everyone to use. There have been technical difficulties with the website for the past two days, and the pages are not displaying properly....
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