Hello,
I am using Achilles dataset (DepMap Public 19Q2) which contains the results of genome-scale CRISPR knockout screen to study the effect of genes in survival and proliferation of certain cancer cell lines. I have a data matrix which contains scores for 17,634 genes across 563 cell lines. I do not understand how to interpret these scores, any help on how to interpret it would be really appreciated.
Thanks!
1 answer
https://www.biorxiv.org/content/10.1101/160861v1
The above paper about CERES was helpful in explaining CERES as a computation method to estimate gene dependency levels which accounts for the copy number specific effect (regions with high CN causes sequence-independent DNA damage and G2 cell-cycle arrest) and variable sgRNA activity. From what I understand, a more negative CERES score indicates depletion of the gene in that cell line, indicating that it is an essential gene for cell viability and a positive score indicates that it is more enriched.
Log in to answer this question.
-
News: Webinar- Target discovery in Alzheimer’s: Linking causal biology with CNS expression
written by Nicole •
-
missing values for batch in RNA-seq data
written by donan •
-
Comparison of ssGSEA scores across different datasets
written by james.zhang20 •
-
Comparing GSEA mutant data to wild type
written by conmul •
-
Can I calculate the correlation of hazard ratios of different features for comparative purposes?
written by joker33 •
-
Known CRISPR KO effects on gene expression
written by j.gleixner •
-
News: Cell Lines: multi-omics network of associations to model precision treatment
written by Pine Biotech •
-
How to favor consistently occurring rare event in CRISPR screen analysis
written by morovatunc
-
Any detailed guides to cancer survival analysis for beginners?
written by jzhou •
-
Determining Up and Down regulated genes from GEO GDS4296
written by hAjmal •
