Dataset heatmap
Hi all, I have a dataset where if I calculate ratio then I can see that the dataset has a very small fold changes (not even 1.5 FC) but when I plot a heatmAp of individual replicates, it’s shows...
View ArticleActivity Area
Hello, I downloaded pharmacological profiling dataset from CCLE named ‘CCLE_NP24.2009_Drug_data_2015.02.24.csv’, but there is a column named ‘ActArea’ which I assume is ‘Activity Area’. Shouldn’t...
View ArticleBasal growth rate of cell line
Is the basal cell line growth rate available with DepMap’s dependency data? 1 post - 1 participant Read full topic
View ArticleA simple question on download
Dear community members, I’m interested in downloading a list of genes when KO’ed by CRISPR, they have crippling effects on pediatric tumors. Perhaps I can select a current dataset (CRISPR DepMap...
View ArticleIs there any paper or tutorial about the updated DEPMAP project.
I only found the original 2017 paper, but don’t know if there’s any update on it. Any description about those files and what do they imply? I read the readme file but still have a hard time...
View ArticleMissing Gene data in Expression Public 24Q2
Specifically, Cell Line Selector expression data for BST2 returns an empty set for all cell lines in 24Q2. 6 posts - 3 participants Read full topic
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PRISM Batch effect
Hi DepMap! I noticed what appears to be a batch effect, and wanted to share - Plotted below are the median PRISM LFCs (primary screen), across all compounds, sorted on DepMap_ID (accessed from the...
View ArticleActivity Area and lnIC50
I have downloaded a pharmacological profiling dataset from CCLE named ‘CCLE_NP24.2009_Drug_data_2015.02.24.csv’, but there is a column named ‘ActArea’ which I assume is ‘Activity Area’. I am trying to...
View ArticleLMFI(log2 median fluorescence intensity values)
What is the meaning of LMFI from PRISM Repurposing Public 24Q2? Does a lower LMFI score of drug-treated group mean more sensitive than a higher LMFI score of control-group? 1 post - 1 participant Read...
View ArticleDoesn’t the HeLa cell line have gene dependency scores?
Hi, always thank you for your help on the valuable datasets. I have a simple question about the gene dependency file. I thought that HeLa(ACH-001086) was one of the most famous cell lines, but I...
View ArticleEGFR hotspot mutations, custom downloads
Only 13 lines have 1 or 2 in the downloaded file of EGFR hotspot mutations, only 3 in lung, much fewer than expected. 1 post - 1 participant Read full topic
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I Need Guidance on Integrating DepMap Data with RNA-seq Analysis for Cancer...
Hello there, I am working on a cancer research project where we are trying to understand the relationship between genetic dependencies and gene expression profiles across different cancer cell lines....
View Articlemeaning of efficacy column in CRISPRInferredGuideEfficacy.csv + a few other...
Hi, In the CRISPRInferredGuideEfficacy.csv file there are sequences of sgRNAs and their efficacies, which If I understood correctly, are the probability (or at least some measurement) of how well they...
View ArticleExpression Controls
Hi, I would like to know which cell lines were used as controls for the expression analysis. This information will help us determine the regulation of different genes in relation to specific cancer...
View ArticleLS180 (ACH-000957) mutations are different between 20Q1 and 23Q4
Dear DepMap team, Two frameshift mutations in KMT2D (g.chr12:49444973_49444974insG and g.chr12:49444978_49444979insTCAAG) were reported in version 20Q1 and are missing in version 23Q4. Any ideas why?...
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Groupby option in v2 of data explorer
Hello! I would like to visualise how a parameter (dependency, expression etc.) varies across lineages (see attached an example extracted from v1 of data explorer). However, I am unable to find the...
View ArticleNegative correlation with gene dependency
How do or where can I download genes that are negatively correlated with gene dependency (ie when a gene of interest is knocked out in a cell type- what genes are predicted to be unregulated in...
View ArticleScript to calculate gene dependencies
Three years ago I used this script provided (Revisions · Script based on code from the DepMap portal code to compute the top N pearson correlations and write to a CSV file · GitHub) to calculate...
View ArticleGNF-7 gene target misnomer
For the compound GNF-7, the Compound Summary says: Metadata from the Repurposing Hub Target/Mechanism: GLUCOKINASE INHIBITOR, PROTEIN KINASE INHIBITOR Target: GCK, [TNK2]TNK2 DepMap Gene Summary) On...
View ArticleEnsembl, Gencode versions for DepMap data
For the recent DepMap release (24Q2) How can we locate/what are the associated ENSEMBL and Gencode versions? Thanks. 1 post - 1 participant Read full topic
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