Optimal Construction of a Functional Interaction Network From Pooled Library CRISPR Fitness Screens

Authors

Veronica Gheorghe
Traver Hart

Publication Date

11-28-2022

Journal

BMC Bioinformatics

Abstract

BACKGROUND: Functional interaction networks, where edges connect genes likely to operate in the same biological process or pathway, can be inferred from CRISPR knockout screens in cancer cell lines. Genes with similar knockout fitness profiles across a sufficiently diverse set of cell line screens are likely to be co-functional, and these "coessentiality" networks are increasingly powerful predictors of gene function and biological modularity. While several such networks have been published, most use different algorithms for each step of the network construction process.

RESULTS: In this study, we identify an optimal measure of functional interaction and test all combinations of options at each step-essentiality scoring, sample variance and covariance normalization, and similarity measurement-to identify best practices for generating a functional interaction network from CRISPR knockout data. We show that Bayes Factor and Ceres scores give the best results, that Ceres outperforms the newer Chronos scoring scheme, and that covariance normalization is a critical step in network construction. We further show that Pearson correlation, mathematically identical to ordinary least squares after covariance normalization, can be extended by using partial correlation to detect and amplify signals from "moonlighting" proteins which show context-dependent interaction with different partners.

CONCLUSIONS: We describe a systematic survey of methods for generating coessentiality networks from the Cancer Dependency Map data and provide a partial correlation-based approach for exploring context-dependent interactions.

Keywords

Clustered Regularly Interspaced Short Palindromic Repeats, Bayes Theorem, Gene Library, Cell Line, Algorithms

Comments

Supplementary Material

PMID: 36443674

DOI

10.1186/s12859-022-05078-y

PMID

36443674

PMCID

PMC9707256

PubMedCentral® Posted Date

November 2022

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes