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2022-10-19 本文已影响0人重拾生活信心

DepMap: The Cancer Dependency Map Project at Broad Institute

Tutorial pdf
Gene dpendency：
A genetic dependency is a gene that is considered necessary for the proliferation and survival of a given cell population.

Gene dependency 图表解读

The dependent cell lines tile

Gene Effect Score ：扰动后的效应。

算法：DEMETER2 (RNAi) or Chronos (CRISPR) 。
normalization：已知的common essential genes 的median effect score为 -1，non-essential 为0，normalization。效应越大，越负。

图中信息
a) the distribution of gene effect scores
b) the fraction of cell lines classified asdependenton the gene
c) a category assigned to each dependency profile when/as appropriate.

根据gene effect score distribution 分成3类基因
1.Strongly Selective Distribution

Strongly Selective Distribution ：在某些cell lines 中 dependent

2.Common-Essential Distribution

Common-Essential Distribution ：在大部分cell lines 中 dependent，-1附近或者更负

3.Non-essential Distribution

Non-essential Distribution ：大部分分布在 0 附近

CRISPR KO vs RNAi Knockdown

differences between
Dependent or Not 的分类
与已知essential、non相比较，计算dependent 的概率，>0.5 则定义为dependent。算法：Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines | bioRxiv