Mutations for entire genes missing
In comparing the OmicsSomaticMutations mutation data between 23Q4 and 23Q2 I’ve found that mutations for multiple genes are now entirely missing. For example all mutations in RAB10 (9 non-silent...
View ArticleDepMap don't have cell line data for HEK-293?
Dear Team, I noticed that the DepMap database seems to be missing cell line data for the widely used HEK-293 cell line. This cell line is quite well-known and commonly employed in various research...
View ArticleMissing AC values in 22Q2 release
Dear DepMap, I am using CCLE data to review RNA mutation data for BRAF. When there are missing AC values in RNA mutation data, should these be interpreted as missing data, or was the alternate allele...
View ArticleThe VAF for a given mutation
Is there anywhere in the mutation data where there is a column showing the variant allele frequency (VAF) for a given mutation in a given cell line? 2 posts - 2 participants Read full topic
View ArticleCRISPRGeneEffect vs. ScreenGeneEffect
What is the difference between these 2 files? - I could not see any differences specified in the README file 1 post - 1 participant Read full topic
View ArticleDiscrepancies between downloaded files and GUI
I see a large difference between the number of distinct(ModelID) in the CRISPRGeneEffect.csv versus the Model.csv download from here. This misalignment doesn’t appear using the GUI Data Explorer. Is...
View ArticlePotential Network Issue with Simultaneous Access to DepMap
While teaching a class using DepMap, I noticed that the DepMap homepage worked fine when I accessed it on my own. However, when students tried to access it simultaneously, it was blocked. I’m...
View ArticleCreating a Data Set of Cell Lines That Have One Gene But Not Another
Hi, I’m trying to download a data set of cell lines that express a certain X chromosome gene but NOT a certain Y chromosome gene. I was wondering if there was any way to do this through DepMap. Thanks...
View ArticleSRY gene KO is scored in multiple cell lines originating from women
I couldn’t help but notice that the DepMap CRISPR KO score is assigned for SRY gene in cell lines originating from women. Presumably, most of them have no Y chromosome where SRY is localized....
View ArticleChronos versus CERES gene score difference
Hi! There’s a significant difference in gene score between CERES (~-0.7) and Chronos (~-0.1), for my gene of interest in a large subset of cell lines. Is there a way to understand which algorithm is...
View ArticleIdentification of tumor suppressor genes
Hi, I have a question about gene effect score and gene dependency score. Does essentiality only mean that knocking out a gene will cause cancer cells to stop growing or even die? Is there a reverse...
View Articleurgent help needed
Hello, I am new to depmap and i am finding it hard interpreting the data, specially the T-statistic value for genes and P values, what they imply? I am trying to look at essential genes in a cancer...
View Articlegene expression values in CCLE miRNA datasets
Hi folks! I am trying to explore the correlation among a protein-coding gene, a LncRNA, and a microRNA among lung cancer cell lines. CCLE2019 datasets seem to suit my needs. But I got a little...
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PRISM Repurposing Public 23Q2 two-class comparison shift from 0
I did a two-class comparison for the PRISM Repurposing Public 23Q2 data for a few lineages of interest and found that the distribution of effect sizes is not centering at 0 (whereas in the Skyros...
View ArticleAnnouncing the 24Q2 Release
OVERVIEW We’re excited to release new Omics and CRISPR data to the DepMap portal, as well as updated portal tools, like Data Explorer 2, and a new data hub where you can learn more about DepMap’s data...
View ArticleRNAi (Achilles+DRIVE+Marcotte, DEMETER2) meaning
Hello, I want to identify HER2 positive breast cancer cell lines. I downloaded the relevant file from DepMap and created column for ERBB2 (NGL, c-ERB-2, HER-2, c-ERB2, CD340, NEU, MLN-19, p185(erbB2),...
View ArticleDepmap portal down
For the past two days it seems like nothing on Depmap is loading. It’ll open the front page but if I try to select any of the tabs or look up a gene I get a blank screen as if it’s going to load in...
View ArticleUploading a list of cell lines into Cell line selector or Context Manager
For the new release, it appears we can no longer upload a list of depmap IDs or cell line names into the cell line selector. Is this correct or am I missing where to upload a list of Depmap IDs for...
View ArticleIssue with custom analysis volcano plot in the 24Q2 portal update
Today, a user reported an inconsistency between correlations reported by the volcano plot and the scatter plot in DE2. Upon investigating we discovered a bug stemming from the way that data was...
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...
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