Investigate the expression level of a gene in defined groups
I would like to know how to use data explorer to make a plot of Gene A expression between high Gene B expression and low Gene B expression. 1 post - 1 participant Read full topic
View ArticleUnable to Download Files - "PRISM Repurposing Secondary Screen"
I am unable to download any files from “PRISM Repurposing Secondary Screen”, other files can be downloaded normally. I tried switching networks and VPN, changing devices, and using different browsers...
View ArticleDrug screening data (PRISM) vs. CRISPR screening data
Hi, I have a simple question about the results after drug screening and CRISPR screening. TL;DR Can the values in those screenings be considered in the same context? To my knowledge, the...
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Discrepency in front-end data and back-end data in 'Enriched Lineages' section
SIRPA Issue For the target 'SIRPA' the front end shows: But when we calculate the p-values using t-test for this target, there is no p-value for any of the cell-lines. The code to get the p-value is...
View ArticleCRISPR KO screens
We did our first CRISPR Cas9 KO screen with 2 cancer cell lines of interest in the lab and wanted to compare our results to the ones available at DepMap. I used the MAGeCK-VISPR tool to identify...
View ArticleMocs3 interacting drugs
Hello, I am a 3rd year PhD student looking to understand how can I look for the CRISPR libraries and select an existing compound that could inhibit my gene of interest MOCS3. If you could help me out...
View ArticleUnable to open anything
Trying to choose cell lines based on their GNA13 expression in the pancreas. Unable to open compare expression distribution page and anything else relating to expression. Error received when trying to...
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Drug screen data is not availbale or is it chnaged the way we used to access it
Dear DepMap members, I am interested in checking the drug sensitivity of melanoma lines to atorvastatin drug and other drugs in relation to the LDLR protein levels. In the past I used to see the...
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Details of CRISPR experiment: ScreenSequenceMap.csv
Hello, I would like to know the specific process of conducting CRISPR experiments on DepMap However, I couldn’t find the ScreenSequenceMap.csv mentioned on the webpage. I also tried other search...
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Prism secondary drug screening unable to download (google cloud access denied)
Hi DepMap team, Looks like we are all unable to download the PRISM secondary drug screening results. My error message is “google cloud access denied”. Could you please help solve this issue? Thank you...
View ArticleMetadata for ssGSEA pathways
Hello all, I am having trouble finding information about the gene set enrichment pathways (columns) in ssGSEA_Public_24Q2_subsetted. For example, I would like to know which genes are included in each...
View ArticleAnnotation version for each release
Hi everyone, I have been looking through different GitHub pages and different parts of the website, but I couldn’t locate a page for the annotation used for each release. Is there a page where the...
View ArticleWGS MAF file
Where can I find mutation data for HCC1143 WGS regions? The OmicsSomaticMutations file I downloaded seems to be mostly covering exonic regions and very few intronic regions and I’m actually interested...
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Row names in the OmicsExpressionTranscripts file
Hi, I have a simple question about the OmicsExpressionTranscriptsTPMLogp1Profile file. When I tried to match the row names in it to the model name, I couldn’t find the related information in...
View ArticleCo-dependency lists?
Was wondering if there is a place I can download the full CRISPR co-dependencies (not just top 100), meaning the correlations from DepMap Public 24Q4+Score, Chronos, for all genes? 1 post - 1...
View ArticleBatch corrected Expression Public 24Q4 - What base?
Hey! I am unsure what base the Batch corrected Expression Public 24Q4 expression data comes in. I used the “Create and download a customized dataset” page and selected/downloaded the Batch corrected...
View Articlelist of essential genes for the survival of colorectal cancer cells
I am a data scientist and have recently started working with biological data. I need some guidance: Which version of the dataset should I use to obtain the list of essential genes for the survival of...
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Mesenchymal models
A while ago, I performed a DepMap analysis to find the mean gene effect on Meshenchymal models, as shown in the attached image. Currently, I’m trying to repeat the same query using different...
View ArticleCell Line Selection for CRISPR Screen
Hi, This may be a very naive question - apologies in advance. Any help would be much appreciated. I’m trying to design a CRISPR base-editing screen for a list of oncogenes and tumorsupressors. I’m...
View ArticleAvailability of RNA-seq data after drug treatment
Hello, I am looking for RNA-seq data of cancer cell lines treated with specific drugs. Could you please provide information on where I can find these datasets within DepMap or if they are available...
View ArticleMultiple SMILES in secondary-screen-dose-response-curve-parameters.csv
Hello, I hope this message finds you well. I am currently working with the dataset in the file secondary-screen-dose-response-curve-parameters.csv and noticed that the “smiles” column contains...
View ArticleAvailability of of RNA-seq bigwig files
Hello, I am looking for RNA-seq genome-wide coverage data in bigwig format (instead of table with expression per gene). Is this level of data available? Or a level of data that could be converted to...
View ArticleNormalization -TMM
Hi I want to understand that if I have to do TMM normalization rather than using TPM as TPM is not considered a very good parameter to compare across different samples. Which file with Raw reads would...
View ArticleNegative goodness of fit
Dear DepMap team, Why some r2 values in the Prism secondary-screen-dose-response-curve-parameters.csv file are negative? Isn’t r2 bounded between 0 and 1? Thanks 1 post - 1 participant Read full topic
View ArticleNon-breaking space in Model.csv current version (2024Q4)
Hi - Minor but I hit a potential problem using the current (2024Q4) version of Model.csv. For the entry for model ID ACH-000938, for the field ModelSubtypeFeatures, it contains “DUX4” and then some...
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error in custom analysis
I’m trying to compare the CRISPR dependencies of one cell line vs two other cell lines. It returns an unexpected error. 2 posts - 2 participants Read full topic
View ArticleIC50 unit of measure
Hi, In the file “Drug_sensitivity_AUC_(CTD^2)_subsetted” Are the IC50 values informed in micromolar? If so, what do negative values mean? Was the concentratation range (7.8-2000 nM) the same for all...
View ArticleGDSC or CTD2 data in data explorer?
Hi As always great to have DepMap and the Data Explorer tool! Question - in Data Explorer it seems I’m able to drug screen data just for the PRISM screens (which are great) but not GDSC or CTD2. Is...
View ArticleAvailability of VCF/WGS data for cell line demultiplexing
Hi all, I am working with a single-cell RNA-seq experiment where two cell lines, HT29 (COAD) and KP4 (Pancreas), were multiplexed together before sequencing. The data has been aligned to the GRCh38...
View ArticleTACC3 AO-252 Phase 1A
A2A Pharmaceuticals has a TACC3 inhibitor in phase 1 for ovarian, triple negative and endometrial cancers. Based on complete regressions preclinically, for these indications as well as gastric and...
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